## Load functions
source("~/Documents/RegGenoLab/COVID19/pyscenic/regulons-selection-scripts/regs-analysis.R")
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
## ✔ ggplot2 3.3.5     ✔ purrr   0.3.4
## ✔ tibble  3.1.7     ✔ dplyr   1.0.9
## ✔ tidyr   1.2.0     ✔ stringr 1.4.0
## ✔ readr   2.1.2     ✔ forcats 0.5.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## Loading required package: grid
## ========================================
## ComplexHeatmap version 2.8.0
## Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
## Github page: https://github.com/jokergoo/ComplexHeatmap
## Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
## 
## If you use it in published research, please cite:
## Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
##   genomic data. Bioinformatics 2016.
## 
## The new InteractiveComplexHeatmap package can directly export static 
## complex heatmaps into an interactive Shiny app with zero effort. Have a try!
## 
## This message can be suppressed by:
##   suppressPackageStartupMessages(library(ComplexHeatmap))
## ========================================
## ========================================
## circlize version 0.4.14
## CRAN page: https://cran.r-project.org/package=circlize
## Github page: https://github.com/jokergoo/circlize
## Documentation: https://jokergoo.github.io/circlize_book/book/
## 
## If you use it in published research, please cite:
## Gu, Z. circlize implements and enhances circular visualization
##   in R. Bioinformatics 2014.
## 
## This message can be suppressed by:
##   suppressPackageStartupMessages(library(circlize))
## ========================================
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:dplyr':
## 
##     combine, intersect, setdiff, union
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
##     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
##     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
##     union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:dplyr':
## 
##     first, rename
## The following object is masked from 'package:tidyr':
## 
##     expand
## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
## The following objects are masked from 'package:dplyr':
## 
##     collapse, desc, slice
## The following object is masked from 'package:purrr':
## 
##     reduce
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:dplyr':
## 
##     select
## 
## 
## 
## Attaching package: 'enrichplot'
## The following object is masked from 'package:ggpubr':
## 
##     color_palette
## clusterProfiler v4.0.5  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
## 
## If you use clusterProfiler in published research, please cite:
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. doi: 10.1016/j.xinn.2021.100141
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:AnnotationDbi':
## 
##     select
## The following object is masked from 'package:IRanges':
## 
##     slice
## The following object is masked from 'package:S4Vectors':
## 
##     rename
## The following object is masked from 'package:purrr':
## 
##     simplify
## The following object is masked from 'package:stats':
## 
##     filter


Selection of Regulons based on Differentially Activation and Specificity

Use of Regulon Specificity Scores (also referred here as enrichment although it is not exactly) + Differential Activation (DA) of Regulons Analysis. This is an exploratory report on the parameters used to select regulons. Main code for Regulons Selection = reticulateEnrich.R


DA tests pvalues distributions

Mann Whitney U Test

P-values distributions resulting from Mann Whitney U Test for Differential Activation of Regulons (measured from AUC scores per regulon, Regulon Activity Matrix). Non-adjusted p-values are displayed.

Run reticulateEnrich_.R first.

library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange

pvalues <- as.data.frame(read_csv(paste0(params$inputdir,params$pval_mwu.fn), col_names = T))
# rename cols for display in graphs
if(params$celllines==1){
  names(pvalues) <- str_replace(names(pvalues), "SARS-CoV-2", "SARSCoV2")
  names(pvalues) <- str_replace(names(pvalues), "w_vector_expressing_", "")
  names(pvalues) <- str_replace(names(pvalues), "1hr_Ruxolitinib_pre-treatment", "pt")
}

plots <- vector('list', length(pvalues)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues)) {
  exp <- colnames(pvalues)[i]
  print(exp)
  
  plots[[i]] <- ggplot(pvalues,aes(x=.data[[exp]])) + #<<
    geom_bar(fill="#9966bb") + # geom hist didnt work
    scale_x_binned() +
    labs(title = exp, x="pvalue", y="")
}
## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu-3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"
names(plots) <- names(pvalues)
# display plots together
p <- ggarrange(plots[[1]],plots[[2]],plots[[3]],plots[[4]],plots[[5]], plots[[6]],
          ncol = 2, nrow = 3)
# add title
annotate_figure(p, 
                top = text_grob("P-values Mann Whitney U Tests",face = "bold", size = 14))

## save to png
png(paste0(params$outdir,"hist_pvalues-mwu_01.png"), width = 600, height = 600)
p
dev.off()
## png 
##   2
p <- ggarrange(plots[[8]],plots[[7]],plots[[9]],plots[[10]],plots[[11]],
          ncol = 2, nrow = 3)
# add title
annotate_figure(p, 
                top = text_grob("P-values Mann Whitney U Tests",face = "bold", size = 14))

png(paste0(params$outdir,"hist_pvalues-mwu_02.png"))
p
dev.off()
## png 
##   2
# minimum p values per experiment
apply(pvalues,2,min)
##             HPIV3_infected_A549               IAV_infected_A549 
##                    0.0001770350                    0.0003325123 
##               IAV_infected_NHBE           IAVdNS1_infected_NHBE 
##                    0.0031276088                    0.0031276088 
##               RSV_infected_A549          SARSCoV2_infected_A549 
##                    0.0002334267                    0.0000737137 
##    SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt 
##                    0.0021645022                    0.0091157873 
##        SARSCoV2_infected_Calu-3          SARSCoV2_infected_NHBE 
##                    0.0636025696                    0.0050437189 
##         human_IFNB_treated_NHBE 
##                    0.0011655012

Each pvalue corresponds to a TF/regulon being differentially active in a given experiment vs its control (not shown).

  • pvalues from TRUE null hypothesis (corresponding to Error Type II) distribution –> uniform distribution in range [0,1]

  • pvalues from FALSE null hypothesis distribution –> asymetric, skewed to zero

Most of these distributions show that pvalues are more skewed to zero than what we would expect from a uniform distribution thus indicating that most of them correspond to FALSE null hypothesis.

Using a too low significance level would lead to rejecting true positives.[1]

However, the exception is the case of SARS-CoV-2 infected A549 expressing hACE2, where the pvalues distribution is flattened, with a skew towards 1. A strict significance level should be used in this case.

Kolmogrov Test

P-values distributions resulting from Kolmogrov Test for Differential Activation of Regulons (measured from AUC scores per regulon, Regulon Activity Matrix). Non-adjusted p-values are displayed.

library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange


pvalues2 <- as.data.frame(read_csv(paste0(params$inputdir,params$pval_klm.fn), col_names = T))
# rename cols for display in graphs
names(pvalues2) <- names(pvalues)

plots2 <- vector('list', length(pvalues2)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues2)) {
  exp <- colnames(pvalues2)[i]
  print(exp)
  
  plots2[[i]] <- ggplot(pvalues2,aes(x=.data[[exp]])) + #<<
    geom_bar(fill="#9966bb") + # geom hist didnt work
    scale_x_binned() +
    labs(title = exp, x="pvalue", y="")
  
}
## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu-3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"
names(plots2) <- names(pvalues2)

# display plots together
p <- ggarrange(plots2[[1]],plots2[[2]],plots2[[3]],plots2[[4]],plots2[[5]], plots2[[6]],
          ncol = 2, nrow = 3)
# add title
annotate_figure(p, 
                top = text_grob("P-values Kolmogrov Tests ",face = "bold", size = 14))

png(paste0(params$outdir,"hist_pvalues-klm_01.png"), width = 600, height = 600)
p
dev.off()
## png 
##   2
p <- ggarrange(plots2[[8]],plots2[[7]],plots2[[9]],plots2[[10]],plots2[[11]],
            ncol = 2, nrow = 3)
# add title
annotate_figure(p, 
                top = text_grob("P-values Kolmogrov Tests",face = "bold", size = 14))

png(paste0(params$outdir,"hist_pvalues-klm_02.png"), width = 600, height = 600)
p
dev.off()
## png 
##   2
apply(pvalues,2,min)
##             HPIV3_infected_A549               IAV_infected_A549 
##                    0.0001770350                    0.0003325123 
##               IAV_infected_NHBE           IAVdNS1_infected_NHBE 
##                    0.0031276088                    0.0031276088 
##               RSV_infected_A549          SARSCoV2_infected_A549 
##                    0.0002334267                    0.0000737137 
##    SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt 
##                    0.0021645022                    0.0091157873 
##        SARSCoV2_infected_Calu-3          SARSCoV2_infected_NHBE 
##                    0.0636025696                    0.0050437189 
##         human_IFNB_treated_NHBE 
##                    0.0011655012

DA tests adjusted pvalues distributions

Mann Whitney U Test

Get dataframes of adjusted pvalues from both test to work with locally:

# on the cluster
# Run `reticulateEnrich_.R` first
library(tidyverse)

# retrieve adjusted pvalues from difregs script
pvalues_adj <- py$pvalues_adjusted
pvalues_adj2 <- py$pvalues_adjusted2


# turn to dataframes
pv.adj.mwu <- t(data.frame(matrix(unlist(pvalues_adj), nrow=length(pvalues_adj), byrow=TRUE)))
colnames(pv.adj.mwu) <- keys_ct
pv.adj.klm <- t(data.frame(matrix(unlist(pvalues_adj2), nrow=length(pvalues_adj2), byrow=TRUE)))
colnames(pv.adj.klm) <- keys_ct
if(celllines==1){
  colnames(pv.adj.mwu) <- str_replace_all(colnames(pv.adj.mwu), "-", "")
  colnames(pv.adj.mwu) <- str_replace(colnames(pv.adj.mwu), "w_vector_expressing_", "")
  colnames(pv.adj.mwu) <- str_replace(colnames(pv.adj.mwu), "1hr_Ruxolitinib_pretreatment", "pt")
  colnames(pv.adj.klm) <- colnames(pv.adj.mwu)
}

write.csv(pv.adj.mwu, file = paste0(outdir,"pvalues-mwu-2t-adjusted.csv"), quote = F, row.names = F)
write.csv(pv.adj.mwu, file = paste0(outdir,"pvalues-klm-2t-adjusted.csv"), quote = F, row.names = F)

Make plots:

library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange

pv.adj.mwu <- as.data.frame(
  read_csv(file = paste0(params$inputdir,params$adj_pvals_mwu.fn),col_names = T))
## Rows: 898 Columns: 11
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (11): HPIV3_infected_A549, IAV_infected_A549, IAV_infected_NHBE, IAVdNS1...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
pvalues <- pv.adj.mwu # just changed this #<<

# rename cols for display in graphs
if(params$celllines==1){
  names(pvalues) <- str_replace(names(pvalues), "SARS-CoV-2", "SARSCoV2")
  names(pvalues) <- str_replace(names(pvalues), "w_vector_expressing_", "")
  names(pvalues) <- str_replace(names(pvalues), "1hr_Ruxolitinib_pre-treatment", "pt")
}

plots <- vector('list', length(pvalues)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues)) {
  exp <- colnames(pvalues)[i]
  print(exp)
  
  plots[[i]] <- ggplot(pvalues,aes(x=.data[[exp]])) + #<<
    geom_bar(fill="#9966bb") + # geom hist didnt work
    scale_x_binned() +
    labs(title = exp, x="pvalue", y="")
  
}
## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"
names(plots) <- names(pvalues)


# display plots together
p <- ggarrange(plots[[1]],plots[[2]],plots[[3]],plots[[4]],plots[[5]], plots[[6]],
          ncol = 2, nrow = 3)
# add title
annotate_figure(p, 
                top = text_grob("Adjusted P-values Mann Whitney U Tests",
                                face = "bold", size = 14)) # and this

png(paste0(params$outdir,"hist_adj-pvalues-mwu_01.png"), width = 600, height = 600)
p
dev.off()
## png 
##   2
p <- ggarrange(plots[[8]],plots[[7]],plots[[9]],plots[[10]],plots[[11]],
            ncol = 2, nrow = 3)
annotate_figure(p,top = text_grob("Adjusted P-values Mann Whitney U Tests",face = "bold", size = 14)) # and this

png(paste0(params$outdir,"hist_pvalues-mwu_02.png"), width = 600, height = 600)
p
dev.off()
## png 
##   2
# minimum p values per experiment
apply(pvalues,2,min)
##             HPIV3_infected_A549               IAV_infected_A549 
##                     0.039744348                     0.021328286 
##               IAV_infected_NHBE           IAVdNS1_infected_NHBE 
##                     0.024405490                     0.024965249 
##               RSV_infected_A549          SARSCoV2_infected_A549 
##                     0.016124398                     0.002364104 
##    SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt 
##                     0.080988456                     0.130623943 
##         SARSCoV2_infected_Calu3          SARSCoV2_infected_NHBE 
##                     0.237566138                     0.106146572 
##         human_IFNB_treated_NHBE 
##                     0.037379287

Kolmogrov Test

library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange

pv.adj.klm <- as.data.frame(read_csv(paste0(params$inputdir,params$adj_pvals_klm.fn), col_names = T))
pvalues2 <- pv.adj.klm # just changed this #<<

# rename cols for display in graphs
names(pvalues2) <- names(pvalues)

plots2 <- vector('list', length(pvalues2)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues2)) {
  exp <- colnames(pvalues2)[i]
  print(exp)
  
  plots2[[i]] <- ggplot(pvalues2,aes(x=.data[[exp]])) + #<<
    geom_bar(fill="#9966bb") + # geom hist didnt work
    scale_x_binned() +
    labs(title = exp, x="pvalue", y="")
  
}
## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"
names(plots2) <- names(pvalues2)

# display plots together
p <- ggarrange(plots2[[1]],plots2[[2]],plots2[[3]],plots2[[4]],plots2[[5]], plots2[[6]],
        ncol = 2, nrow = 3)
# add title
annotate_figure(p, 
                top = text_grob("Adjusted P-values Kolmogrov Tests",
                                face = "bold", size = 14)) # and this

png(paste0(params$outdir,"hist_adj-pvalues-klm_01.png"), width = 600, height = 600)
p
dev.off()
## png 
##   2
p <- ggarrange(plots2[[8]],plots2[[7]],plots2[[9]],plots2[[10]],plots2[[11]],
          ncol = 2, nrow = 3)
# add title
annotate_figure(p, 
                top = text_grob("Adjusted P-values Kolmogrov Tests",
                                face = "bold", size = 14)) # and this

png(paste0(params$outdir,"hist_adj-pvalues-klm_02.png"), width = 600, height = 600)
p
dev.off()
## png 
##   2
apply(pvalues,2,min)
##             HPIV3_infected_A549               IAV_infected_A549 
##                     0.039744348                     0.021328286 
##               IAV_infected_NHBE           IAVdNS1_infected_NHBE 
##                     0.024405490                     0.024965249 
##               RSV_infected_A549          SARSCoV2_infected_A549 
##                     0.016124398                     0.002364104 
##    SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt 
##                     0.080988456                     0.130623943 
##         SARSCoV2_infected_Calu3          SARSCoV2_infected_NHBE 
##                     0.237566138                     0.106146572 
##         human_IFNB_treated_NHBE 
##                     0.037379287

FDR threshold on adjusted p-values

Mann Whitney U Test

Import dataset and call source script with functions:

library(tidyverse)

## call functios
source("~/Documents/RegGenoLab/COVID19/PulmonDB_COVID/COVID/bulk/rScripts/FDRthreshold_functions.R")

## dataset
pv.adj.mwu <- as.data.frame(read_csv(paste0(params$inputdir,params$adj_pvals_mwu.fn), col_names = T))
pv.adj.mwu <- as.data.frame(pv.adj.mwu)
# rename cols for display in graphs
if(params$celllines==1){
  names(pv.adj.mwu) <- str_replace(names(pv.adj.mwu), "SARS-CoV-2", "SARSCoV2")
  names(pv.adj.mwu) <- str_replace(names(pv.adj.mwu), "w_vector_expressing_", "")
  names(pv.adj.mwu) <- str_replace(names(pv.adj.mwu), "1hr_Ruxolitinib_pre-treatment", "pt")
}
#head(pv.adj.mwu)
thrs.mwu <- regsPerFDRthr(pv.adj.mwu, fdr_lowth = 0.1, fdr_upthr = 0.24)
thrs.mwu

Se buscó que el FDR threshold (entre 0.2 y 0.1) elegido permitiera que nos quedaramos con alrededor de 100 regulones por experimento. Esto puesto que el set de regulones se someterá a otros filtros: - pvalor ajustado en test de Kolmogrov - LFC de enriquecimiento de regulon en el experimento dado En conjunto, estos filtros darán lugar a un set de regulones cuya especificidad y relevancia en el experimento dado sean relativamente confiables.

El FDR threshold elegido por experimento se especifica aquí:

fdrs.mwu <- getChosenFDRth(thrs.mwu, min.regs = c(100,30))
fdrs.mwu

Kolmogrov Test

thrs.klm <- regsPerFDRthr(pv.adj.klm, fdr_lowth = 0.1, fdr_upthr = 0.24)
thrs.klm

El FDR threshold elegido por experimento se especifica aquí:

fdrs.klm <- getChosenFDRth(thrs.klm, min.regs = c(100,30))
fdrs.klm

Regulons Counts After Filtering


DA:

After taking common Differentialy Activated Regulons from both tests:

tfs_da.fn <- paste0(params$inputdir, params$tfs_DA_2t.fn)
tfs_da <- readRDS(tfs_da.fn)
# at reticulateEnrich line 117
## check how many regulons were kept
t(as.data.frame(lapply(tfs_da,length)))
##                                 [,1]
## HPIV3_infected_A549              123
## IAV_infected_A549                243
## IAV_infected_NHBE                287
## IAVdNS1_infected_NHBE            287
## RSV_infected_A549                 47
## SARSCoV2_infected_A549           222
## SARSCoV2_infected_A549_hACE2      29
## SARSCoV2_infected_A549_hACE2_pt  184
## SARSCoV2_infected_Calu3          378
## SARSCoV2_infected_NHBE           141
## human_IFNB_treated_NHBE           31

✅ Filter Applied


Differentiate between Up and Down Regulated regulons based on logFC (infection/mock):

library(tidyverse)

## Load Data
# auc_mtx 
auc_mtx <- readRDS(paste0(params$inputdir,params$auc_mtx))

# Load data: TFs names (in order after just scenic counts cutoff)
tfs <- as.data.frame(read_csv(paste0(params$inputdir,params$tfs.fn), col_names = F))[,1]
## Rows: 898 Columns: 1
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (1): X1
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
tfs <- stringr::str_remove(tfs, "_\\(\\+\\)")
tfs <- tfs[match(str_remove(colnames(auc_mtx),"_\\(\\+\\)"), tfs)]

# Load and tidy data: log 2 FC (auc_mtx)
l2fc <- as.data.frame(read_csv(paste0(params$inputdir,params$l2fc.fn), col_names = T))
## Rows: 898 Columns: 11
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (11): HPIV3_infected_A549, IAV_infected_A549, IAV_infected_NHBE, IAVdNS1...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
if(params$celllines==1){
  names(l2fc) <- str_replace_all(names(l2fc), "-", "")
  names(l2fc) <- str_replace(names(l2fc), "w_vector_expressing_", "")
  names(l2fc) <- str_replace(names(l2fc), "1hr_Ruxolitinib_pretreatment", "pt")
}
rownames(l2fc) <- colnames(auc_mtx)
head(l2fc)
## match dfs rows (tfs)
l2fc <- l2fc[match(str_replace(tfs,"$","_\\(\\+\\)"),rownames(l2fc)),]

## Make lists of up/down regulons
tfs_da_up = list()
tfs_da_down = list()
for (exp in names(tfs_da)) {
  tfs_da_up[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in%  rownames(l2fc)[which(l2fc[exp] > 0)]]
  tfs_da_down[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in% rownames(l2fc)[which(l2fc[exp] < 0)]]
}

# make df of counts of regulons
n_up <- t(as.data.frame(lapply(tfs_da_up,length)))[,1]
n_down <- t(as.data.frame(lapply(tfs_da_down,length)))[,1]
data.frame(up = n_up, down = n_down)

✅ Filter Applied for Upregulated Regulons


DA + specificity:

After filtering regulons for those that had an optimal LFC enrichment :

tfs_da_enrich.fn <- paste0(params$inputdir, params$tfs_DA_enrichLFC_2t.fn)
tfs_da_enrich <- readRDS(tfs_da_enrich.fn)
names(tfs_da_enrich) <- names(tfs_da)
# at reticulateEnrich line 117
## check how many regulons were kept
t(as.data.frame(lapply(tfs_da_enrich,length)))
##                                 [,1]
## HPIV3_infected_A549                2
## IAV_infected_A549                  1
## IAV_infected_NHBE                 75
## IAVdNS1_infected_NHBE            123
## RSV_infected_A549                  0
## SARSCoV2_infected_A549             9
## SARSCoV2_infected_A549_hACE2      17
## SARSCoV2_infected_A549_hACE2_pt   13
## SARSCoV2_infected_Calu3          202
## SARSCoV2_infected_NHBE             7
## human_IFNB_treated_NHBE           24


Differentiate between Up and Down Regulated regulons again:

## Make lists of up/down regulons
tfs_da_enrich_up = list()
tfs_da_enrich_down = list()
for (exp in names(tfs_da_enrich)) {
  tfs_da_enrich_up[[exp]] <- 
    tfs_da_enrich[[exp]][tfs_da_enrich[[exp]] %in% rownames(l2fc)[which(l2fc[exp] > 0)]]
  tfs_da_enrich_down[[exp]] <- 
    tfs_da_enrich[[exp]][tfs_da_enrich[[exp]] %in% rownames(l2fc)[which(l2fc[exp] < 0)]]
}

# make df of counts of regulons
n_up <- t(as.data.frame(lapply(tfs_da_enrich_up,length)))[,1]
n_down <- t(as.data.frame(lapply(tfs_da_enrich_down,length)))[,1]
data.frame(up = n_up, down = n_down)

For regulons that were Upregulated and enriched, this filter keeps a decent number of regulons, but that’s not the case for Downregulated regulons.

✅ Filter Applied for Upregulated Regulons

Volcano Plots

library(ggplot2)
library(ggrepel)

############################################
## Plots 2t - 2 tails test

# Load and tidy data: regulons/tfs that were in DA + enriched 
paste0("using set of DA regulons (tfs): ",tfs_da.fn)
## [1] "using set of DA regulons (tfs): ../regulons-analysis/out/celllines/tfs_mwu_ks_fdr1-24-2t.RData"
tfs_da.fn <- paste0(params$inputdir, params$tfs_DA_2t.fn)
tfs_da <- readRDS(tfs_da.fn)
if(params$celllines==1){
  names(tfs_da) <- str_replace_all(names(tfs_da), "-", "")
  names(tfs_da) <- str_replace(names(tfs_da), "_w_vector_expressing", "")
  names(tfs_da) <- str_replace(names(tfs_da), "1hr_Ruxolitinib_pretreatment", "pt")
}
tfs_da
## $HPIV3_infected_A549
##   [1] "ALX3_(+)"    "ALX4_(+)"    "ARNT_(+)"    "ARNTL_(+)"   "ATF1_(+)"   
##   [6] "ATF4_(+)"    "ATF5_(+)"    "BCL6B_(+)"   "BHLHE40_(+)" "BHLHE41_(+)"
##  [11] "BRF1_(+)"    "CDX1_(+)"    "CHD2_(+)"    "CLOCK_(+)"   "CPEB1_(+)"  
##  [16] "CREB1_(+)"   "CREB5_(+)"   "DDIT3_(+)"   "DLX2_(+)"    "E2F1_(+)"   
##  [21] "E4F1_(+)"    "ELF2_(+)"    "ESRRA_(+)"   "FOSL1_(+)"   "FOXA2_(+)"  
##  [26] "FOXB1_(+)"   "FOXC2_(+)"   "FOXF2_(+)"   "FOXK1_(+)"   "FOXO1_(+)"  
##  [31] "FOXO3_(+)"   "FOXP2_(+)"   "GABPB1_(+)"  "GCM1_(+)"    "HAND1_(+)"  
##  [36] "HES6_(+)"    "HEY1_(+)"    "HEY2_(+)"    "HIVEP2_(+)"  "HLF_(+)"    
##  [41] "HOXA9_(+)"   "HOXB2_(+)"   "HOXB6_(+)"   "HOXB8_(+)"   "HOXB9_(+)"  
##  [46] "HOXC10_(+)"  "HOXC13_(+)"  "HOXC8_(+)"   "HOXD11_(+)"  "HSF2_(+)"   
##  [51] "IKZF2_(+)"   "IRF4_(+)"    "ISL2_(+)"    "KDM5A_(+)"   "KLF3_(+)"   
##  [56] "KLF7_(+)"    "KLF9_(+)"    "LHX4_(+)"    "MAF_(+)"     "MAZ_(+)"    
##  [61] "MECOM_(+)"   "MXD3_(+)"    "MXI1_(+)"    "MYCN_(+)"    "MYEF2_(+)"  
##  [66] "NEUROD1_(+)" "NFE2L1_(+)"  "NFIA_(+)"    "NFIL3_(+)"   "NFKB1_(+)"  
##  [71] "NFKB2_(+)"   "NFYA_(+)"    "NFYC_(+)"    "NHLH1_(+)"   "NKX3-1_(+)" 
##  [76] "NR2C1_(+)"   "NR5A2_(+)"   "OTP_(+)"     "PAX7_(+)"    "POU3F2_(+)" 
##  [81] "POU5F1_(+)"  "RARB_(+)"    "RFX2_(+)"    "RFX3_(+)"    "RREB1_(+)"  
##  [86] "RUNX2_(+)"   "SNAI3_(+)"   "SOX1_(+)"    "SOX15_(+)"   "SP6_(+)"    
##  [91] "TAF7_(+)"    "TAGLN2_(+)"  "TAL1_(+)"    "TBX15_(+)"   "TBX20_(+)"  
##  [96] "TCF3_(+)"    "TFE3_(+)"    "TFEB_(+)"    "THAP1_(+)"   "VSX1_(+)"   
## [101] "ZBTB33_(+)"  "ZBTB7A_(+)"  "ZEB1_(+)"    "ZFX_(+)"     "ZIC2_(+)"   
## [106] "ZNF134_(+)"  "ZNF143_(+)"  "ZNF148_(+)"  "ZNF160_(+)"  "ZNF227_(+)" 
## [111] "ZNF354C_(+)" "ZNF429_(+)"  "ZNF449_(+)"  "ZNF502_(+)"  "ZNF524_(+)" 
## [116] "ZNF571_(+)"  "ZNF597_(+)"  "ZNF607_(+)"  "ZNF668_(+)"  "ZNF672_(+)" 
## [121] "ZNF787_(+)"  "ZNF841_(+)"  "ZSCAN26_(+)"
## 
## $IAV_infected_A549
##   [1] "ALX1_(+)"     "ALX4_(+)"     "ARNT_(+)"     "ARNT2_(+)"    "ARNTL2_(+)"  
##   [6] "ASCL2_(+)"    "ATF2_(+)"     "ATF4_(+)"     "BACH1_(+)"    "BATF_(+)"    
##  [11] "BBX_(+)"      "BCL11A_(+)"   "BCL11B_(+)"   "BCLAF1_(+)"   "BHLHE40_(+)" 
##  [16] "BRF1_(+)"     "CDX2_(+)"     "CLOCK_(+)"    "CPEB1_(+)"    "CREB5_(+)"   
##  [21] "CTCFL_(+)"    "DLX3_(+)"     "DLX5_(+)"     "E2F1_(+)"     "E2F2_(+)"    
##  [26] "E2F4_(+)"     "E2F5_(+)"     "E2F6_(+)"     "E2F8_(+)"     "EGR1_(+)"    
##  [31] "EGR3_(+)"     "EHF_(+)"      "ELF1_(+)"     "ELF4_(+)"     "ELF5_(+)"    
##  [36] "ELK3_(+)"     "ELK4_(+)"     "EN1_(+)"      "EN2_(+)"      "ERF_(+)"     
##  [41] "ESRRA_(+)"    "ETS1_(+)"     "ETS2_(+)"     "ETV1_(+)"     "ETV7_(+)"    
##  [46] "FOSB_(+)"     "FOSL2_(+)"    "FOXB1_(+)"    "FOXC1_(+)"    "FOXD3_(+)"   
##  [51] "FOXF2_(+)"    "FOXM1_(+)"    "FOXO1_(+)"    "GABPA_(+)"    "GABPB1_(+)"  
##  [56] "GATA5_(+)"    "GCM1_(+)"     "GLI1_(+)"     "GLIS2_(+)"    "GRHL1_(+)"   
##  [61] "GRHL3_(+)"    "GRHPR_(+)"    "GSC_(+)"      "GSX2_(+)"     "GTF2B_(+)"   
##  [66] "GTF2IRD1_(+)" "HES1_(+)"     "HES5_(+)"     "HES6_(+)"     "HIC1_(+)"    
##  [71] "HINFP_(+)"    "HIVEP2_(+)"   "HLX_(+)"      "HNF1A_(+)"    "HNF1B_(+)"   
##  [76] "HOXA1_(+)"    "HOXA2_(+)"    "HOXA5_(+)"    "HOXA6_(+)"    "HOXA7_(+)"   
##  [81] "HOXA9_(+)"    "HOXB13_(+)"   "HOXB5_(+)"    "HOXB7_(+)"    "HOXB8_(+)"   
##  [86] "HOXC10_(+)"   "HOXC11_(+)"   "HOXC13_(+)"   "HOXC5_(+)"    "HOXC6_(+)"   
##  [91] "HOXD3_(+)"    "HOXD4_(+)"    "HOXD9_(+)"    "HTATIP2_(+)"  "IRF1_(+)"    
##  [96] "IRF2_(+)"     "IRF3_(+)"     "IRF5_(+)"     "IRF6_(+)"     "IRF7_(+)"    
## [101] "IRF9_(+)"     "IRX1_(+)"     "IRX2_(+)"     "IRX4_(+)"     "IRX5_(+)"    
## [106] "JUND_(+)"     "KLF10_(+)"    "KLF3_(+)"     "KLF4_(+)"     "KLF5_(+)"    
## [111] "KLF6_(+)"     "KLF8_(+)"     "KLF9_(+)"     "LBX2_(+)"     "LHX2_(+)"    
## [116] "LHX5_(+)"     "LMX1B_(+)"    "MAFA_(+)"     "MAFB_(+)"     "MAFG_(+)"    
## [121] "MAX_(+)"      "MAZ_(+)"      "MECOM_(+)"    "MEOX1_(+)"    "MNX1_(+)"    
## [126] "MSX2_(+)"     "MTF1_(+)"     "MXD1_(+)"     "MXD3_(+)"     "MXD4_(+)"    
## [131] "MXI1_(+)"     "MYCN_(+)"     "MYEF2_(+)"    "MYPOP_(+)"    "MZF1_(+)"    
## [136] "NEUROD1_(+)"  "NFATC4_(+)"   "NFE2_(+)"     "NFE2L1_(+)"   "NFIA_(+)"    
## [141] "NFKB1_(+)"    "NFYA_(+)"     "NFYC_(+)"     "NHLH2_(+)"    "NKX2-1_(+)"  
## [146] "NKX3-1_(+)"   "NR1H3_(+)"    "NR1H4_(+)"    "NR2E1_(+)"    "NR2F1_(+)"   
## [151] "NR2F6_(+)"    "ONECUT2_(+)"  "OTP_(+)"      "OTX1_(+)"     "OVOL2_(+)"   
## [156] "PAX7_(+)"     "PAX9_(+)"     "PHF21A_(+)"   "PHF8_(+)"     "PKNOX1_(+)"  
## [161] "POLE4_(+)"    "POLR2A_(+)"   "POLR3A_(+)"   "POLR3G_(+)"   "POU2F1_(+)"  
## [166] "POU2F3_(+)"   "POU3F1_(+)"   "POU3F4_(+)"   "PPARD_(+)"    "PRDM1_(+)"   
## [171] "PRDM15_(+)"   "PRRX2_(+)"    "PSMD12_(+)"   "RAB18_(+)"    "RARG_(+)"    
## [176] "REL_(+)"      "RFX2_(+)"     "RORA_(+)"     "RREB1_(+)"    "RXRG_(+)"    
## [181] "SATB1_(+)"    "SETDB1_(+)"   "SIN3A_(+)"    "SIX2_(+)"     "SIX5_(+)"    
## [186] "SMAD1_(+)"    "SMARCA5_(+)"  "SMARCC2_(+)"  "SNAI2_(+)"    "SNAI3_(+)"   
## [191] "SOX5_(+)"     "SP3_(+)"      "SP5_(+)"      "STAT1_(+)"    "STAT2_(+)"   
## [196] "STAT5A_(+)"   "STAT5B_(+)"   "TAGLN2_(+)"   "TBPL2_(+)"    "TCF12_(+)"   
## [201] "TCF3_(+)"     "TCF7_(+)"     "TEAD4_(+)"    "TEF_(+)"      "TFAP2A_(+)"  
## [206] "TFAP2C_(+)"   "TFAP2E_(+)"   "TFDP2_(+)"    "TGIF2_(+)"    "TLX2_(+)"    
## [211] "TRIM28_(+)"   "USF1_(+)"     "USF2_(+)"     "VAX1_(+)"     "VDR_(+)"     
## [216] "VSX2_(+)"     "ZBTB7A_(+)"   "ZFX_(+)"      "ZNF134_(+)"   "ZNF143_(+)"  
## [221] "ZNF208_(+)"   "ZNF219_(+)"   "ZNF274_(+)"   "ZNF281_(+)"   "ZNF35_(+)"   
## [226] "ZNF354C_(+)"  "ZNF426_(+)"   "ZNF429_(+)"   "ZNF471_(+)"   "ZNF483_(+)"  
## [231] "ZNF502_(+)"   "ZNF524_(+)"   "ZNF554_(+)"   "ZNF560_(+)"   "ZNF597_(+)"  
## [236] "ZNF672_(+)"   "ZNF682_(+)"   "ZNF720_(+)"   "ZNF729_(+)"   "ZNF730_(+)"  
## [241] "ZNF761_(+)"   "ZNF773_(+)"   "ZNF787_(+)"  
## 
## $IAV_infected_NHBE
##   [1] "AHCTF1_(+)"       "AIRE_(+)"         "ALX1_(+)"        
##   [4] "ALX3_(+)"         "ALX4_(+)"         "AR_(+)"          
##   [7] "ARID5B_(+)"       "ARNT_(+)"         "ARNTL2_(+)"      
##  [10] "ATF1_(+)"         "ATF3_(+)"         "BACH2_(+)"       
##  [13] "BATF_(+)"         "BCL3_(+)"         "BCLAF1_(+)"      
##  [16] "BDP1_(+)"         "BHLHE41_(+)"      "BNC2_(+)"        
##  [19] "BORCS8-MEF2B_(+)" "BRF1_(+)"         "CCNT2_(+)"       
##  [22] "CDX2_(+)"         "CEBPA_(+)"        "CEBPB_(+)"       
##  [25] "CEBPD_(+)"        "CELF6_(+)"        "CHD2_(+)"        
##  [28] "CKMT1B_(+)"       "CLOCK_(+)"        "CNOT3_(+)"       
##  [31] "CPEB1_(+)"        "CPSF4_(+)"        "CREB1_(+)"       
##  [34] "CREB3_(+)"        "CREB3L1_(+)"      "CUX1_(+)"        
##  [37] "DBX1_(+)"         "DLX2_(+)"         "DLX4_(+)"        
##  [40] "DMRT1_(+)"        "DMRTA1_(+)"       "DUXA_(+)"        
##  [43] "E2F3_(+)"         "E2F4_(+)"         "E2F6_(+)"        
##  [46] "EGR1_(+)"         "EGR2_(+)"         "EGR3_(+)"        
##  [49] "ELK3_(+)"         "EMX1_(+)"         "EN1_(+)"         
##  [52] "EN2_(+)"          "ENO1_(+)"         "EP300_(+)"       
##  [55] "ERF_(+)"          "ESRRA_(+)"        "ESRRB_(+)"       
##  [58] "ETV1_(+)"         "ETV3_(+)"         "ETV5_(+)"        
##  [61] "EVX2_(+)"         "FGF19_(+)"        "FOS_(+)"         
##  [64] "FOSL1_(+)"        "FOXA1_(+)"        "FOXA2_(+)"       
##  [67] "FOXB1_(+)"        "FOXC1_(+)"        "FOXC2_(+)"       
##  [70] "FOXD2_(+)"        "FOXD3_(+)"        "FOXD4_(+)"       
##  [73] "FOXD4L6_(+)"      "FOXF2_(+)"        "FOXJ2_(+)"       
##  [76] "FOXK1_(+)"        "FOXK2_(+)"        "FOXM1_(+)"       
##  [79] "FOXN1_(+)"        "FOXO1_(+)"        "FOXO3_(+)"       
##  [82] "FOXO6_(+)"        "FOXQ1_(+)"        "GATA3_(+)"       
##  [85] "GCM1_(+)"         "GLIS2_(+)"        "GMEB1_(+)"       
##  [88] "GRHL2_(+)"        "GTF2IRD1_(+)"     "HAND1_(+)"       
##  [91] "HDAC1_(+)"        "HES5_(+)"         "HEY1_(+)"        
##  [94] "HINFP_(+)"        "HLF_(+)"          "HMGB1_(+)"       
##  [97] "HNF1A_(+)"        "HNF1B_(+)"        "HOXA10_(+)"      
## [100] "HOXA2_(+)"        "HOXA5_(+)"        "HOXA9_(+)"       
## [103] "HOXB13_(+)"       "HOXB4_(+)"        "HOXB6_(+)"       
## [106] "HOXB8_(+)"        "HOXB9_(+)"        "HOXC10_(+)"      
## [109] "HOXC13_(+)"       "HOXC4_(+)"        "HOXC6_(+)"       
## [112] "HOXC8_(+)"        "HOXC9_(+)"        "HOXD11_(+)"      
## [115] "HOXD13_(+)"       "HOXD3_(+)"        "HOXD4_(+)"       
## [118] "HSF2_(+)"         "HSF4_(+)"         "HTATIP2_(+)"     
## [121] "IKZF3_(+)"        "ING3_(+)"         "IRF1_(+)"        
## [124] "IRF4_(+)"         "IRX2_(+)"         "IRX5_(+)"        
## [127] "ISL2_(+)"         "JUN_(+)"          "JUNB_(+)"        
## [130] "JUND_(+)"         "KDM5A_(+)"        "KLF1_(+)"        
## [133] "KLF10_(+)"        "KLF11_(+)"        "KLF12_(+)"       
## [136] "KLF13_(+)"        "KLF14_(+)"        "KLF2_(+)"        
## [139] "KLF5_(+)"         "KLF8_(+)"         "LHX4_(+)"        
## [142] "LHX8_(+)"         "LHX9_(+)"         "LMX1B_(+)"       
## [145] "MAF_(+)"          "MAFB_(+)"         "MAFF_(+)"        
## [148] "MAFG_(+)"         "MEF2B_(+)"        "MEF2C_(+)"       
## [151] "MEOX2_(+)"        "MLXIP_(+)"        "MLXIPL_(+)"      
## [154] "MNT_(+)"          "MNX1_(+)"         "MSX1_(+)"        
## [157] "MSX2_(+)"         "MYEF2_(+)"        "MYOD1_(+)"       
## [160] "MZF1_(+)"         "NFATC2_(+)"       "NFE2L2_(+)"      
## [163] "NFE2L3_(+)"       "NFIA_(+)"         "NFIB_(+)"        
## [166] "NFIC_(+)"         "NFIL3_(+)"        "NFKB2_(+)"       
## [169] "NHLH1_(+)"        "NKX2-1_(+)"       "NKX2-5_(+)"      
## [172] "NKX3-1_(+)"       "NPDC1_(+)"        "NR0B1_(+)"       
## [175] "NR1D1_(+)"        "NR2E1_(+)"        "NR2F1_(+)"       
## [178] "NR3C1_(+)"        "NR4A1_(+)"        "NR5A2_(+)"       
## [181] "NR6A1_(+)"        "NRF1_(+)"         "ONECUT1_(+)"     
## [184] "ONECUT2_(+)"      "ONECUT3_(+)"      "OTP_(+)"         
## [187] "PATZ1_(+)"        "PAX7_(+)"         "PDX1_(+)"        
## [190] "PKNOX1_(+)"       "POLE3_(+)"        "POLR2A_(+)"      
## [193] "POLR3G_(+)"       "POU3F2_(+)"       "POU3F4_(+)"      
## [196] "POU5F1_(+)"       "PPARD_(+)"        "PROX1_(+)"       
## [199] "PRRX1_(+)"        "PSMD12_(+)"       "RARB_(+)"        
## [202] "RARG_(+)"         "RBBP5_(+)"        "REL_(+)"         
## [205] "RELA_(+)"         "RFX1_(+)"         "RFX2_(+)"        
## [208] "RFX3_(+)"         "RFX5_(+)"         "RFXAP_(+)"       
## [211] "SATB1_(+)"        "SIN3A_(+)"        "SIX2_(+)"        
## [214] "SIX4_(+)"         "SIX5_(+)"         "SOHLH2_(+)"      
## [217] "SOX1_(+)"         "SOX13_(+)"        "SOX15_(+)"       
## [220] "SOX2_(+)"         "SOX21_(+)"        "SOX4_(+)"        
## [223] "SOX6_(+)"         "SP7_(+)"          "SP9_(+)"         
## [226] "SPDEF_(+)"        "SREBF2_(+)"       "STAT4_(+)"       
## [229] "TAF7_(+)"         "TAGLN2_(+)"       "TAL1_(+)"        
## [232] "TBP_(+)"          "TBPL1_(+)"        "TBX15_(+)"       
## [235] "TBX20_(+)"        "TBX3_(+)"         "TBX6_(+)"        
## [238] "TCF4_(+)"         "TCF7_(+)"         "TET1_(+)"        
## [241] "TFAP2A_(+)"       "TFDP1_(+)"        "TFE3_(+)"        
## [244] "TFEB_(+)"         "THAP1_(+)"        "TLX2_(+)"        
## [247] "TLX3_(+)"         "TRPS1_(+)"        "UQCRB_(+)"       
## [250] "USF2_(+)"         "VEZF1_(+)"        "VSX1_(+)"        
## [253] "VSX2_(+)"         "XBP1_(+)"         "YBX1_(+)"        
## [256] "ZBTB41_(+)"       "ZBTB43_(+)"       "ZEB1_(+)"        
## [259] "ZFHX2_(+)"        "ZIC2_(+)"         "ZNF160_(+)"      
## [262] "ZNF189_(+)"       "ZNF208_(+)"       "ZNF239_(+)"      
## [265] "ZNF263_(+)"       "ZNF264_(+)"       "ZNF274_(+)"      
## [268] "ZNF281_(+)"       "ZNF316_(+)"       "ZNF441_(+)"      
## [271] "ZNF442_(+)"       "ZNF467_(+)"       "ZNF471_(+)"      
## [274] "ZNF486_(+)"       "ZNF502_(+)"       "ZNF513_(+)"      
## [277] "ZNF560_(+)"       "ZNF571_(+)"       "ZNF597_(+)"      
## [280] "ZNF668_(+)"       "ZNF713_(+)"       "ZNF721_(+)"      
## [283] "ZNF740_(+)"       "ZNF816_(+)"       "ZNF836_(+)"      
## [286] "ZSCAN31_(+)"      "ZXDC_(+)"        
## 
## $IAVdNS1_infected_NHBE
##   [1] "AIRE_(+)"     "ALX1_(+)"     "AR_(+)"       "ARNT_(+)"     "ARNTL2_(+)"  
##   [6] "ATF1_(+)"     "ATF3_(+)"     "ATF5_(+)"     "BACH2_(+)"    "BATF_(+)"    
##  [11] "BCL3_(+)"     "BCLAF1_(+)"   "BDP1_(+)"     "BHLHE40_(+)"  "BHLHE41_(+)" 
##  [16] "BNC2_(+)"     "BRF1_(+)"     "CCNT2_(+)"    "CDX2_(+)"     "CEBPA_(+)"   
##  [21] "CEBPB_(+)"    "CEBPD_(+)"    "CELF6_(+)"    "CHD2_(+)"     "CKMT1B_(+)"  
##  [26] "CNOT3_(+)"    "CPSF4_(+)"    "CREB1_(+)"    "CREB3_(+)"    "CREB3L1_(+)" 
##  [31] "CTCF_(+)"     "DBX1_(+)"     "DDIT3_(+)"    "DLX2_(+)"     "E2F3_(+)"    
##  [36] "E2F4_(+)"     "E2F6_(+)"     "E2F8_(+)"     "EGR1_(+)"     "EGR2_(+)"    
##  [41] "EGR3_(+)"     "ELK3_(+)"     "EMX1_(+)"     "EN2_(+)"      "ENO1_(+)"    
##  [46] "EP300_(+)"    "ERF_(+)"      "ESR2_(+)"     "ESRRA_(+)"    "ESRRB_(+)"   
##  [51] "ETV1_(+)"     "ETV3_(+)"     "ETV5_(+)"     "EVX2_(+)"     "FGF19_(+)"   
##  [56] "FOS_(+)"      "FOSL1_(+)"    "FOXA1_(+)"    "FOXA2_(+)"    "FOXB1_(+)"   
##  [61] "FOXC1_(+)"    "FOXC2_(+)"    "FOXD2_(+)"    "FOXD3_(+)"    "FOXD4_(+)"   
##  [66] "FOXD4L4_(+)"  "FOXD4L6_(+)"  "FOXK1_(+)"    "FOXK2_(+)"    "FOXM1_(+)"   
##  [71] "FOXO1_(+)"    "FOXO3_(+)"    "FOXO6_(+)"    "FOXQ1_(+)"    "GATA3_(+)"   
##  [76] "GATA6_(+)"    "GCM1_(+)"     "GMEB1_(+)"    "GMEB2_(+)"    "GPD1_(+)"    
##  [81] "GRHL2_(+)"    "GSX1_(+)"     "GTF2IRD1_(+)" "HAND1_(+)"    "HDAC1_(+)"   
##  [86] "HES5_(+)"     "HIC1_(+)"     "HINFP_(+)"    "HLF_(+)"      "HMGB1_(+)"   
##  [91] "HNF1B_(+)"    "HOXA10_(+)"   "HOXA2_(+)"    "HOXA5_(+)"    "HOXA9_(+)"   
##  [96] "HOXB13_(+)"   "HOXB2_(+)"    "HOXB6_(+)"    "HOXB8_(+)"    "HOXB9_(+)"   
## [101] "HOXC10_(+)"   "HOXC13_(+)"   "HOXC4_(+)"    "HOXC6_(+)"    "HOXC8_(+)"   
## [106] "HOXC9_(+)"    "HOXD11_(+)"   "HOXD13_(+)"   "HOXD3_(+)"    "HOXD4_(+)"   
## [111] "HSF2_(+)"     "HSF4_(+)"     "HTATIP2_(+)"  "IKZF3_(+)"    "ING3_(+)"    
## [116] "IRF1_(+)"     "IRF4_(+)"     "IRX2_(+)"     "IRX5_(+)"     "ISL2_(+)"    
## [121] "JUN_(+)"      "JUNB_(+)"     "JUND_(+)"     "KDM5A_(+)"    "KLF1_(+)"    
## [126] "KLF11_(+)"    "KLF12_(+)"    "KLF14_(+)"    "KLF2_(+)"     "KLF5_(+)"    
## [131] "KLF8_(+)"     "LHX4_(+)"     "LHX8_(+)"     "LHX9_(+)"     "MAF_(+)"     
## [136] "MAFB_(+)"     "MAFF_(+)"     "MAFG_(+)"     "MEF2B_(+)"    "MLXIP_(+)"   
## [141] "MLXIPL_(+)"   "MNT_(+)"      "MNX1_(+)"     "MSX1_(+)"     "MSX2_(+)"    
## [146] "MXD4_(+)"     "MXI1_(+)"     "MYEF2_(+)"    "MYOD1_(+)"    "MYPOP_(+)"   
## [151] "MZF1_(+)"     "NFATC2_(+)"   "NFE2L1_(+)"   "NFE2L2_(+)"   "NFIA_(+)"    
## [156] "NFIB_(+)"     "NFIC_(+)"     "NFIL3_(+)"    "NFKB2_(+)"    "NHLH1_(+)"   
## [161] "NHLH2_(+)"    "NKX2-1_(+)"   "NKX3-1_(+)"   "NPDC1_(+)"    "NR0B1_(+)"   
## [166] "NR1D1_(+)"    "NR2C1_(+)"    "NR2F1_(+)"    "NR4A1_(+)"    "NR5A2_(+)"   
## [171] "NR6A1_(+)"    "NRF1_(+)"     "ONECUT1_(+)"  "ONECUT2_(+)"  "ONECUT3_(+)" 
## [176] "OTP_(+)"      "PATZ1_(+)"    "PAX7_(+)"     "PHF21A_(+)"   "PKNOX1_(+)"  
## [181] "POLE3_(+)"    "POLR2A_(+)"   "POLR3A_(+)"   "POLR3G_(+)"   "POU1F1_(+)"  
## [186] "POU3F2_(+)"   "POU3F4_(+)"   "POU4F3_(+)"   "POU5F1_(+)"   "PPARD_(+)"   
## [191] "PROX1_(+)"    "PSMD12_(+)"   "RARB_(+)"     "RARG_(+)"     "RBBP5_(+)"   
## [196] "REL_(+)"      "RELA_(+)"     "RFX1_(+)"     "RFX2_(+)"     "RFX3_(+)"    
## [201] "RFX5_(+)"     "RFXAP_(+)"    "SHOX2_(+)"    "SIX4_(+)"     "SIX5_(+)"    
## [206] "SMAD3_(+)"    "SNAPC4_(+)"   "SOHLH2_(+)"   "SOX1_(+)"     "SOX13_(+)"   
## [211] "SOX15_(+)"    "SOX21_(+)"    "SOX4_(+)"     "SOX6_(+)"     "SP9_(+)"     
## [216] "SPDEF_(+)"    "SREBF2_(+)"   "STAT4_(+)"    "TAF7_(+)"     "TAGLN2_(+)"  
## [221] "TAL1_(+)"     "TBP_(+)"      "TBPL1_(+)"    "TBX18_(+)"    "TBX20_(+)"   
## [226] "TBX3_(+)"     "TCF4_(+)"     "TCF7_(+)"     "TEF_(+)"      "TET1_(+)"    
## [231] "TFAP2A_(+)"   "TFDP1_(+)"    "TFE3_(+)"     "TFEB_(+)"     "THAP1_(+)"   
## [236] "TLX3_(+)"     "TRPS1_(+)"    "UBP1_(+)"     "UBTF_(+)"     "UQCRB_(+)"   
## [241] "VEZF1_(+)"    "VSX1_(+)"     "VSX2_(+)"     "XBP1_(+)"     "YBX1_(+)"    
## [246] "YY2_(+)"      "ZBTB41_(+)"   "ZBTB43_(+)"   "ZDHHC15_(+)"  "ZEB1_(+)"    
## [251] "ZFHX2_(+)"    "ZFHX3_(+)"    "ZFP64_(+)"    "ZFX_(+)"      "ZIC2_(+)"    
## [256] "ZNF143_(+)"   "ZNF160_(+)"   "ZNF205_(+)"   "ZNF208_(+)"   "ZNF239_(+)"  
## [261] "ZNF25_(+)"    "ZNF263_(+)"   "ZNF264_(+)"   "ZNF274_(+)"   "ZNF281_(+)"  
## [266] "ZNF316_(+)"   "ZNF426_(+)"   "ZNF441_(+)"   "ZNF449_(+)"   "ZNF467_(+)"  
## [271] "ZNF471_(+)"   "ZNF483_(+)"   "ZNF486_(+)"   "ZNF502_(+)"   "ZNF513_(+)"  
## [276] "ZNF560_(+)"   "ZNF571_(+)"   "ZNF597_(+)"   "ZNF668_(+)"   "ZNF713_(+)"  
## [281] "ZNF717_(+)"   "ZNF721_(+)"   "ZNF740_(+)"   "ZNF816_(+)"   "ZNF841_(+)"  
## [286] "ZSCAN31_(+)"  "ZXDC_(+)"    
## 
## $RSV_infected_A549
##  [1] "ARNT_(+)"    "BCLAF1_(+)"  "BHLHE40_(+)" "CDX1_(+)"    "CLOCK_(+)"  
##  [6] "CREB5_(+)"   "ELF2_(+)"    "ELK3_(+)"    "EP300_(+)"   "ETV1_(+)"   
## [11] "ETV3_(+)"    "FOSL2_(+)"   "GMEB1_(+)"   "HEY1_(+)"    "HOXB6_(+)"  
## [16] "IRX2_(+)"    "KLF7_(+)"    "MAX_(+)"     "MNX1_(+)"    "MXD3_(+)"   
## [21] "MYCN_(+)"    "NFATC2_(+)"  "NFKB1_(+)"   "NFYA_(+)"    "NFYC_(+)"   
## [26] "NKX3-1_(+)"  "NR2F1_(+)"   "PKNOX1_(+)"  "POLR3A_(+)"  "POLR3G_(+)" 
## [31] "PPARD_(+)"   "PRDM16_(+)"  "REL_(+)"     "RREB1_(+)"   "SMAD1_(+)"  
## [36] "SNAI3_(+)"   "SP5_(+)"     "TCF7_(+)"    "ZFX_(+)"     "ZNF208_(+)" 
## [41] "ZNF264_(+)"  "ZNF267_(+)"  "ZNF426_(+)"  "ZNF429_(+)"  "ZNF502_(+)" 
## [46] "ZNF560_(+)"  "ZNF773_(+)" 
## 
## $SARSCoV2_infected_A549
##   [1] "ALX1_(+)"     "ALX3_(+)"     "ALX4_(+)"     "ARNT_(+)"     "ARNT2_(+)"   
##   [6] "ARNTL2_(+)"   "ATF2_(+)"     "ATF4_(+)"     "ATF6_(+)"     "BACH1_(+)"   
##  [11] "BBX_(+)"      "BCL11A_(+)"   "BCL11B_(+)"   "BCLAF1_(+)"   "BHLHA15_(+)" 
##  [16] "BHLHE40_(+)"  "BRF1_(+)"     "CDX2_(+)"     "CELF6_(+)"    "CLOCK_(+)"   
##  [21] "CPEB1_(+)"    "CTCFL_(+)"    "DLX3_(+)"     "DLX4_(+)"     "DLX5_(+)"    
##  [26] "DRGX_(+)"     "E2F1_(+)"     "E2F2_(+)"     "E2F4_(+)"     "E2F5_(+)"    
##  [31] "EHF_(+)"      "ELF1_(+)"     "ELK1_(+)"     "ELK3_(+)"     "ELK4_(+)"    
##  [36] "EN1_(+)"      "ERF_(+)"      "ETS1_(+)"     "ETS2_(+)"     "ETV1_(+)"    
##  [41] "ETV3_(+)"     "FEV_(+)"      "FLI1_(+)"     "FOSL2_(+)"    "FOXA3_(+)"   
##  [46] "FOXD2_(+)"    "FOXD3_(+)"    "FOXF2_(+)"    "FOXP4_(+)"    "FOXQ1_(+)"   
##  [51] "GABPA_(+)"    "GABPB1_(+)"   "GATA5_(+)"    "GCM1_(+)"     "GLI1_(+)"    
##  [56] "GLIS2_(+)"    "GRHL3_(+)"    "GRHPR_(+)"    "GSX2_(+)"     "GTF2B_(+)"   
##  [61] "GTF2IRD1_(+)" "GTF3A_(+)"    "HES5_(+)"     "HES6_(+)"     "HEY1_(+)"    
##  [66] "HIC1_(+)"     "HLX_(+)"      "HNF1A_(+)"    "HNF1B_(+)"    "HOXA1_(+)"   
##  [71] "HOXA6_(+)"    "HOXA7_(+)"    "HOXB13_(+)"   "HOXB2_(+)"    "HOXB5_(+)"   
##  [76] "HOXB6_(+)"    "HOXB8_(+)"    "HOXC10_(+)"   "HOXC11_(+)"   "HOXC6_(+)"   
##  [81] "HOXD3_(+)"    "HOXD4_(+)"    "HOXD9_(+)"    "HSF4_(+)"     "HTATIP2_(+)" 
##  [86] "IKZF2_(+)"    "ING3_(+)"     "IRF2_(+)"     "IRF6_(+)"     "IRF9_(+)"    
##  [91] "IRX1_(+)"     "IRX2_(+)"     "IRX4_(+)"     "JUND_(+)"     "KLF10_(+)"   
##  [96] "KLF6_(+)"     "KLF7_(+)"     "KLF8_(+)"     "LBX2_(+)"     "LHX2_(+)"    
## [101] "LMX1B_(+)"    "MAF_(+)"      "MAFA_(+)"     "MAX_(+)"      "MAZ_(+)"     
## [106] "MECOM_(+)"    "MEOX1_(+)"    "MESP1_(+)"    "MNX1_(+)"     "MXD1_(+)"    
## [111] "MXD3_(+)"     "MXI1_(+)"     "MYCN_(+)"     "MYOD1_(+)"    "MYPOP_(+)"   
## [116] "MZF1_(+)"     "NEUROD1_(+)"  "NFATC4_(+)"   "NFE2L1_(+)"   "NFIA_(+)"    
## [121] "NFIB_(+)"     "NFKB1_(+)"    "NFYA_(+)"     "NFYC_(+)"     "NHLH2_(+)"   
## [126] "NKX2-1_(+)"   "NKX2-5_(+)"   "NKX3-1_(+)"   "NR1H3_(+)"    "NR1H4_(+)"   
## [131] "NR2E1_(+)"    "NR2F1_(+)"    "NR2F6_(+)"    "NR6A1_(+)"    "ONECUT2_(+)" 
## [136] "OTP_(+)"      "OTX1_(+)"     "PATZ1_(+)"    "PAX7_(+)"     "PAX9_(+)"    
## [141] "PHF8_(+)"     "PKNOX1_(+)"   "POLE4_(+)"    "POLR2A_(+)"   "POLR3A_(+)"  
## [146] "POLR3G_(+)"   "POU3F4_(+)"   "PRDM1_(+)"    "PRDM15_(+)"   "PRRX2_(+)"   
## [151] "PSMD12_(+)"   "RAB18_(+)"    "RB1_(+)"      "RFX1_(+)"     "RFX2_(+)"    
## [156] "RREB1_(+)"    "RUNX2_(+)"    "RXRG_(+)"     "SATB1_(+)"    "SHOX2_(+)"   
## [161] "SIN3A_(+)"    "SIX5_(+)"     "SMAD1_(+)"    "SMARCA5_(+)"  "SMARCC2_(+)" 
## [166] "SNAI1_(+)"    "SNAI2_(+)"    "SNAI3_(+)"    "SOX5_(+)"     "SP3_(+)"     
## [171] "SP5_(+)"      "SPDEF_(+)"    "STAT1_(+)"    "STAT5B_(+)"   "TAL2_(+)"    
## [176] "TCF3_(+)"     "TCF7L1_(+)"   "TCF7L2_(+)"   "TEAD2_(+)"    "TFAP2A_(+)"  
## [181] "TFAP2C_(+)"   "TFDP2_(+)"    "THRA_(+)"     "TLX1_(+)"     "TLX2_(+)"    
## [186] "TRIM28_(+)"   "USF1_(+)"     "USF2_(+)"     "VAX1_(+)"     "VSX2_(+)"    
## [191] "ZFHX3_(+)"    "ZFP64_(+)"    "ZFX_(+)"      "ZIC2_(+)"     "ZNF134_(+)"  
## [196] "ZNF143_(+)"   "ZNF219_(+)"   "ZNF267_(+)"   "ZNF281_(+)"   "ZNF319_(+)"  
## [201] "ZNF35_(+)"    "ZNF354C_(+)"  "ZNF426_(+)"   "ZNF429_(+)"   "ZNF471_(+)"  
## [206] "ZNF483_(+)"   "ZNF486_(+)"   "ZNF502_(+)"   "ZNF513_(+)"   "ZNF524_(+)"  
## [211] "ZNF554_(+)"   "ZNF560_(+)"   "ZNF583_(+)"   "ZNF597_(+)"   "ZNF672_(+)"  
## [216] "ZNF720_(+)"   "ZNF729_(+)"   "ZNF730_(+)"   "ZNF75A_(+)"   "ZNF768_(+)"  
## [221] "ZNF773_(+)"   "ZNF787_(+)"  
## 
## $SARSCoV2_infected_A549_hACE2
##  [1] "ATF3_(+)"    "CEBPD_(+)"   "DLX2_(+)"    "EGR3_(+)"    "EMX1_(+)"   
##  [6] "ETV6_(+)"    "ETV7_(+)"    "FOXK1_(+)"   "HIVEP2_(+)"  "HOXB6_(+)"  
## [11] "IRF1_(+)"    "IRF5_(+)"    "IRF8_(+)"    "IRF9_(+)"    "KLF13_(+)"  
## [16] "MEF2B_(+)"   "NEUROD2_(+)" "NFE2L2_(+)"  "NKX3-1_(+)"  "RXRG_(+)"   
## [21] "SMARCA5_(+)" "SOX2_(+)"    "SOX21_(+)"   "STAT1_(+)"   "STAT2_(+)"  
## [26] "TP53_(+)"    "TP73_(+)"    "XBP1_(+)"    "ZNF768_(+)" 
## 
## $SARSCoV2_infected_A549_hACE2_pt
##   [1] "AIRE_(+)"    "AKR1A1_(+)"  "ALX4_(+)"    "ARID5B_(+)"  "ARNT_(+)"   
##   [6] "ATF3_(+)"    "BCLAF1_(+)"  "BHLHA15_(+)" "BHLHE40_(+)" "BRF2_(+)"   
##  [11] "CDX2_(+)"    "CEBPA_(+)"   "CEBPD_(+)"   "CLOCK_(+)"   "CTCFL_(+)"  
##  [16] "DLX2_(+)"    "DLX3_(+)"    "DLX4_(+)"    "DMRT1_(+)"   "DMRTA1_(+)" 
##  [21] "E2F1_(+)"    "E2F2_(+)"    "E2F7_(+)"    "E2F8_(+)"    "EBF1_(+)"   
##  [26] "EGR1_(+)"    "EHF_(+)"     "ELF1_(+)"    "ELF4_(+)"    "ELK3_(+)"   
##  [31] "ELK4_(+)"    "EMX1_(+)"    "ENO1_(+)"    "ERF_(+)"     "ETS1_(+)"   
##  [36] "ETS2_(+)"    "ETV6_(+)"    "ETV7_(+)"    "FOSB_(+)"    "FOSL2_(+)"  
##  [41] "FOXB1_(+)"   "FOXD3_(+)"   "FOXK1_(+)"   "FOXK2_(+)"   "FOXM1_(+)"  
##  [46] "FOXN1_(+)"   "FOXO1_(+)"   "FOXP1_(+)"   "GATA5_(+)"   "GLI1_(+)"   
##  [51] "GRHPR_(+)"   "GSC2_(+)"    "GTF2B_(+)"   "HES6_(+)"    "HEY1_(+)"   
##  [56] "HIVEP2_(+)"  "HLX_(+)"     "HNF4G_(+)"   "HOXA2_(+)"   "HOXA6_(+)"  
##  [61] "HOXA9_(+)"   "HOXB1_(+)"   "HOXB6_(+)"   "HOXC11_(+)"  "HOXC5_(+)"  
##  [66] "HOXC9_(+)"   "HOXD4_(+)"   "HSF1_(+)"    "IKZF2_(+)"   "IRF1_(+)"   
##  [71] "IRF2_(+)"    "IRF5_(+)"    "IRF6_(+)"    "IRF7_(+)"    "IRF8_(+)"   
##  [76] "IRF9_(+)"    "IRX5_(+)"    "JUND_(+)"    "KDM4D_(+)"   "KLF13_(+)"  
##  [81] "KLF5_(+)"    "KLF6_(+)"    "KLF7_(+)"    "LHX1_(+)"    "LHX2_(+)"   
##  [86] "LMX1B_(+)"   "MAFB_(+)"    "MAX_(+)"     "MAZ_(+)"     "MLXIP_(+)"  
##  [91] "MLXIPL_(+)"  "MNX1_(+)"    "MXD3_(+)"    "MYCN_(+)"    "MYEF2_(+)"  
##  [96] "MZF1_(+)"    "NEUROD2_(+)" "NFATC2_(+)"  "NFE2L1_(+)"  "NFE2L2_(+)" 
## [101] "NFKB1_(+)"   "NKX2-2_(+)"  "NKX3-1_(+)"  "NPDC1_(+)"   "NR1D1_(+)"  
## [106] "NR1H3_(+)"   "NR1H4_(+)"   "NR2F1_(+)"   "NR2F6_(+)"   "NR3C2_(+)"  
## [111] "NR4A1_(+)"   "ONECUT2_(+)" "PBX3_(+)"    "PDX1_(+)"    "PHF21A_(+)" 
## [116] "POLE4_(+)"   "POLR3A_(+)"  "POLR3G_(+)"  "POU2F3_(+)"  "POU3F1_(+)" 
## [121] "POU3F4_(+)"  "PPARD_(+)"   "PRDM16_(+)"  "PRRX1_(+)"   "PRRX2_(+)"  
## [126] "REL_(+)"     "RFX1_(+)"    "RFXAP_(+)"   "RUNX2_(+)"   "RXRG_(+)"   
## [131] "SATB1_(+)"   "SETDB1_(+)"  "SHOX2_(+)"   "SIX2_(+)"    "SIX5_(+)"   
## [136] "SMARCA5_(+)" "SMARCC2_(+)" "SNAI3_(+)"   "SOX2_(+)"    "SOX21_(+)"  
## [141] "SOX9_(+)"    "SP6_(+)"     "SREBF1_(+)"  "STAT1_(+)"   "STAT2_(+)"  
## [146] "STAT5B_(+)"  "TAF1_(+)"    "TBX20_(+)"   "TBX3_(+)"    "TCF12_(+)"  
## [151] "TEAD2_(+)"   "TET1_(+)"    "TFAP2A_(+)"  "TFAP2C_(+)"  "TGIF1_(+)"  
## [156] "TP73_(+)"    "TRIM28_(+)"  "TWIST1_(+)"  "USF1_(+)"    "VAX1_(+)"   
## [161] "VEZF1_(+)"   "XBP1_(+)"    "ZBED1_(+)"   "ZBTB41_(+)"  "ZFHX3_(+)"  
## [166] "ZFX_(+)"     "ZNF239_(+)"  "ZNF274_(+)"  "ZNF276_(+)"  "ZNF460_(+)" 
## [171] "ZNF502_(+)"  "ZNF524_(+)"  "ZNF579_(+)"  "ZNF583_(+)"  "ZNF652_(+)" 
## [176] "ZNF668_(+)"  "ZNF672_(+)"  "ZNF701_(+)"  "ZNF721_(+)"  "ZNF730_(+)" 
## [181] "ZNF768_(+)"  "ZNF773_(+)"  "ZNF787_(+)"  "ZXDC_(+)"   
## 
## $SARSCoV2_infected_Calu3
##   [1] "AKR1A1_(+)"       "ALX4_(+)"         "AR_(+)"          
##   [4] "ARID3C_(+)"       "ARID5B_(+)"       "ARNT_(+)"        
##   [7] "ARNT2_(+)"        "ARNTL_(+)"        "ARNTL2_(+)"      
##  [10] "ARX_(+)"          "ASCL1_(+)"        "ASCL2_(+)"       
##  [13] "ATF3_(+)"         "ATF4_(+)"         "ATF6_(+)"        
##  [16] "ATF6B_(+)"        "BACH2_(+)"        "BATF_(+)"        
##  [19] "BBX_(+)"          "BCL11A_(+)"       "BCL3_(+)"        
##  [22] "BDP1_(+)"         "BHLHE40_(+)"      "BHLHE41_(+)"     
##  [25] "BNC2_(+)"         "BORCS8-MEF2B_(+)" "BRCA1_(+)"       
##  [28] "BRF2_(+)"         "CCNT2_(+)"        "CDX2_(+)"        
##  [31] "CEBPD_(+)"        "CEBPG_(+)"        "CIC_(+)"         
##  [34] "CPEB1_(+)"        "CREB3L1_(+)"      "CREB5_(+)"       
##  [37] "CREBL2_(+)"       "CTCF_(+)"         "CUX1_(+)"        
##  [40] "DBP_(+)"          "DDIT3_(+)"        "DLX2_(+)"        
##  [43] "DLX3_(+)"         "DLX4_(+)"         "DMRT1_(+)"       
##  [46] "DRGX_(+)"         "DUX4_(+)"         "DUXA_(+)"        
##  [49] "E2F1_(+)"         "E2F2_(+)"         "E2F8_(+)"        
##  [52] "E4F1_(+)"         "EGR2_(+)"         "EGR3_(+)"        
##  [55] "EHF_(+)"          "ELF1_(+)"         "ELF4_(+)"        
##  [58] "ELK1_(+)"         "ELK3_(+)"         "ELK4_(+)"        
##  [61] "EMX1_(+)"         "ENO1_(+)"         "EOMES_(+)"       
##  [64] "EP300_(+)"        "ESRRA_(+)"        "ESX1_(+)"        
##  [67] "ETS1_(+)"         "ETS2_(+)"         "ETV3_(+)"        
##  [70] "ETV4_(+)"         "ETV6_(+)"         "ETV7_(+)"        
##  [73] "EVX2_(+)"         "FBXL19_(+)"       "FEV_(+)"         
##  [76] "FOSB_(+)"         "FOSL1_(+)"        "FOSL2_(+)"       
##  [79] "FOXA2_(+)"        "FOXA3_(+)"        "FOXC1_(+)"       
##  [82] "FOXC2_(+)"        "FOXD2_(+)"        "FOXD3_(+)"       
##  [85] "FOXD4L6_(+)"      "FOXF1_(+)"        "FOXF2_(+)"       
##  [88] "FOXG1_(+)"        "FOXJ2_(+)"        "FOXJ3_(+)"       
##  [91] "FOXK1_(+)"        "FOXL1_(+)"        "FOXM1_(+)"       
##  [94] "FOXN1_(+)"        "FOXO1_(+)"        "FOXO3_(+)"       
##  [97] "FOXO4_(+)"        "GABPB1_(+)"       "GATA2_(+)"       
## [100] "GATA3_(+)"        "GATA5_(+)"        "GATA6_(+)"       
## [103] "GBX1_(+)"         "GLI1_(+)"         "GLIS2_(+)"       
## [106] "GMEB1_(+)"        "GMEB2_(+)"        "GRHL1_(+)"       
## [109] "GRHL2_(+)"        "GRHPR_(+)"        "GSC_(+)"         
## [112] "GSC2_(+)"         "GTF2B_(+)"        "GTF2IRD1_(+)"    
## [115] "GTF3A_(+)"        "HAND1_(+)"        "HDAC2_(+)"       
## [118] "HES1_(+)"         "HES5_(+)"         "HES6_(+)"        
## [121] "HESX1_(+)"        "HEY2_(+)"         "HINFP_(+)"       
## [124] "HIVEP1_(+)"       "HIVEP2_(+)"       "HLF_(+)"         
## [127] "HLX_(+)"          "HMGB1_(+)"        "HNF1A_(+)"       
## [130] "HOXA2_(+)"        "HOXA6_(+)"        "HOXA9_(+)"       
## [133] "HOXB4_(+)"        "HOXB6_(+)"        "HOXB7_(+)"       
## [136] "HOXB8_(+)"        "HOXB9_(+)"        "HOXC10_(+)"      
## [139] "HOXC11_(+)"       "HOXC13_(+)"       "HOXC4_(+)"       
## [142] "HOXC6_(+)"        "HOXC8_(+)"        "HOXD1_(+)"       
## [145] "HOXD10_(+)"       "HOXD4_(+)"        "HOXD8_(+)"       
## [148] "HOXD9_(+)"        "HSF1_(+)"         "HSF2_(+)"        
## [151] "IKZF2_(+)"        "ING3_(+)"         "IRF1_(+)"        
## [154] "IRF2_(+)"         "IRF4_(+)"         "IRF5_(+)"        
## [157] "IRF6_(+)"         "IRF7_(+)"         "IRF8_(+)"        
## [160] "IRF9_(+)"         "IRX2_(+)"         "ISL2_(+)"        
## [163] "JUN_(+)"          "JUND_(+)"         "KDM4D_(+)"       
## [166] "KDM5A_(+)"        "KLF10_(+)"        "KLF11_(+)"       
## [169] "KLF12_(+)"        "KLF13_(+)"        "KLF14_(+)"       
## [172] "KLF15_(+)"        "KLF16_(+)"        "KLF2_(+)"        
## [175] "KLF5_(+)"         "KLF6_(+)"         "KLF7_(+)"        
## [178] "KLF8_(+)"         "KLF9_(+)"         "LBX1_(+)"        
## [181] "LHX1_(+)"         "LHX4_(+)"         "LHX5_(+)"        
## [184] "LMX1B_(+)"        "MAFA_(+)"         "MAFB_(+)"        
## [187] "MAFK_(+)"         "MAX_(+)"          "MAZ_(+)"         
## [190] "MECOM_(+)"        "MEF2C_(+)"        "MEIS1_(+)"       
## [193] "MEOX2_(+)"        "MESP1_(+)"        "MIOS_(+)"        
## [196] "MITF_(+)"         "MLXIP_(+)"        "MLXIPL_(+)"      
## [199] "MXI1_(+)"         "MYBL1_(+)"        "MYCN_(+)"        
## [202] "MYEF2_(+)"        "MYOD1_(+)"        "MYPOP_(+)"       
## [205] "MZF1_(+)"         "NEUROD1_(+)"      "NFATC2_(+)"      
## [208] "NFE2_(+)"         "NFE2L1_(+)"       "NFE2L2_(+)"      
## [211] "NFE2L3_(+)"       "NFIC_(+)"         "NFKB1_(+)"       
## [214] "NFYA_(+)"         "NFYC_(+)"         "NHLH1_(+)"       
## [217] "NHLH2_(+)"        "NKX3-1_(+)"       "NKX6-2_(+)"      
## [220] "NPAS2_(+)"        "NPDC1_(+)"        "NR0B1_(+)"       
## [223] "NR1H2_(+)"        "NR1H3_(+)"        "NR1H4_(+)"       
## [226] "NR1I2_(+)"        "NR2E1_(+)"        "NR2F1_(+)"       
## [229] "NR2F6_(+)"        "NR4A1_(+)"        "NR5A2_(+)"       
## [232] "NRF1_(+)"         "OLIG2_(+)"        "OLIG3_(+)"       
## [235] "ONECUT2_(+)"      "OTP_(+)"          "OVOL1_(+)"       
## [238] "PAX7_(+)"         "PAX8_(+)"         "PAX9_(+)"        
## [241] "PBX1_(+)"         "PDX1_(+)"         "PHF2_(+)"        
## [244] "PHF21A_(+)"       "PHF8_(+)"         "PHOX2A_(+)"      
## [247] "PKNOX1_(+)"       "POLE3_(+)"        "POLR2A_(+)"      
## [250] "POLR3A_(+)"       "POU2F1_(+)"       "POU4F1_(+)"      
## [253] "POU5F1_(+)"       "POU5F1B_(+)"      "POU6F1_(+)"      
## [256] "PPARA_(+)"        "PPARD_(+)"        "PRDM1_(+)"       
## [259] "PRDM16_(+)"       "PRRX1_(+)"        "PRRX2_(+)"       
## [262] "RAD21_(+)"        "RARA_(+)"         "RARG_(+)"        
## [265] "RBBP5_(+)"        "REL_(+)"          "RFX7_(+)"        
## [268] "RREB1_(+)"        "RUNX2_(+)"        "SATB1_(+)"       
## [271] "SETDB1_(+)"       "SHOX2_(+)"        "SIN3A_(+)"       
## [274] "SIX1_(+)"         "SIX2_(+)"         "SIX5_(+)"        
## [277] "SMAD1_(+)"        "SMARCA5_(+)"      "SMARCC2_(+)"     
## [280] "SMC3_(+)"         "SNAI3_(+)"        "SNAPC4_(+)"      
## [283] "SOX11_(+)"        "SOX13_(+)"        "SOX15_(+)"       
## [286] "SOX2_(+)"         "SOX21_(+)"        "SOX4_(+)"        
## [289] "SOX9_(+)"         "SP1_(+)"          "SP2_(+)"         
## [292] "SP6_(+)"          "SP7_(+)"          "SP9_(+)"         
## [295] "SPDEF_(+)"        "SREBF2_(+)"       "SRF_(+)"         
## [298] "STAT1_(+)"        "STAT2_(+)"        "STAT4_(+)"       
## [301] "STAT5B_(+)"       "STAU2_(+)"        "TAF7_(+)"        
## [304] "TAL1_(+)"         "TBP_(+)"          "TBPL2_(+)"       
## [307] "TBX15_(+)"        "TBX18_(+)"        "TBX20_(+)"       
## [310] "TBX6_(+)"         "TCF3_(+)"         "TCF4_(+)"        
## [313] "TCF7_(+)"         "TCF7L1_(+)"       "TEAD4_(+)"       
## [316] "TET1_(+)"         "TFAP2A_(+)"       "TFAP2C_(+)"      
## [319] "TFDP1_(+)"        "TFDP2_(+)"        "TFE3_(+)"        
## [322] "TFEB_(+)"         "TGIF2_(+)"        "THAP1_(+)"       
## [325] "TLX1_(+)"         "TLX2_(+)"         "TP73_(+)"        
## [328] "TRIM28_(+)"       "UBP1_(+)"         "USF1_(+)"        
## [331] "VAX1_(+)"         "VAX2_(+)"         "VDR_(+)"         
## [334] "VEZF1_(+)"        "VSX1_(+)"         "VSX2_(+)"        
## [337] "WT1_(+)"          "YBX1_(+)"         "YY2_(+)"         
## [340] "ZBTB33_(+)"       "ZEB1_(+)"         "ZFHX2_(+)"       
## [343] "ZFY_(+)"          "ZNF134_(+)"       "ZNF143_(+)"      
## [346] "ZNF160_(+)"       "ZNF208_(+)"       "ZNF219_(+)"      
## [349] "ZNF25_(+)"        "ZNF264_(+)"       "ZNF267_(+)"      
## [352] "ZNF276_(+)"       "ZNF316_(+)"       "ZNF354C_(+)"     
## [355] "ZNF384_(+)"       "ZNF429_(+)"       "ZNF441_(+)"      
## [358] "ZNF471_(+)"       "ZNF483_(+)"       "ZNF486_(+)"      
## [361] "ZNF513_(+)"       "ZNF524_(+)"       "ZNF550_(+)"      
## [364] "ZNF554_(+)"       "ZNF560_(+)"       "ZNF606_(+)"      
## [367] "ZNF607_(+)"       "ZNF668_(+)"       "ZNF672_(+)"      
## [370] "ZNF713_(+)"       "ZNF717_(+)"       "ZNF721_(+)"      
## [373] "ZNF761_(+)"       "ZNF768_(+)"       "ZNF787_(+)"      
## [376] "ZNF8_(+)"         "ZSCAN31_(+)"      "ZXDC_(+)"        
## 
## $SARSCoV2_infected_NHBE
##   [1] "AHCTF1_(+)"  "AIRE_(+)"    "ALX1_(+)"    "ARID5B_(+)"  "ARNT_(+)"   
##   [6] "ATF1_(+)"    "BATF_(+)"    "BBX_(+)"     "BCL3_(+)"    "BCL6B_(+)"  
##  [11] "CEBPB_(+)"   "CEBPG_(+)"   "CKMT1B_(+)"  "CREB1_(+)"   "CREB3_(+)"  
##  [16] "CREBL2_(+)"  "DLX4_(+)"    "DMRT1_(+)"   "DMRTA1_(+)"  "DUXA_(+)"   
##  [21] "EBF1_(+)"    "EGR2_(+)"    "ERF_(+)"     "ESRRA_(+)"   "ETV1_(+)"   
##  [26] "ETV6_(+)"    "ETV7_(+)"    "FOSL1_(+)"   "FOXA2_(+)"   "FOXF2_(+)"  
##  [31] "FOXK2_(+)"   "FOXP3_(+)"   "FOXQ1_(+)"   "GATA2_(+)"   "GATA3_(+)"  
##  [36] "HDAC2_(+)"   "HES5_(+)"    "HLF_(+)"     "HNF1A_(+)"   "HNF1B_(+)"  
##  [41] "HOXA2_(+)"   "HOXA5_(+)"   "HOXA7_(+)"   "HOXA9_(+)"   "HOXB5_(+)"  
##  [46] "HOXB6_(+)"   "HOXB7_(+)"   "HOXB8_(+)"   "HOXB9_(+)"   "HOXC10_(+)" 
##  [51] "HOXC4_(+)"   "HOXC5_(+)"   "HOXC6_(+)"   "HOXC8_(+)"   "HSF2_(+)"   
##  [56] "ING3_(+)"    "IRF1_(+)"    "IRF3_(+)"    "IRF4_(+)"    "IRF5_(+)"   
##  [61] "IRF8_(+)"    "IRF9_(+)"    "IRX2_(+)"    "ISL2_(+)"    "JUN_(+)"    
##  [66] "KLF10_(+)"   "KLF5_(+)"    "LHX1_(+)"    "LHX4_(+)"    "LHX8_(+)"   
##  [71] "LHX9_(+)"    "MAFF_(+)"    "MEOX2_(+)"   "MIOS_(+)"    "MLXIP_(+)"  
##  [76] "MSX1_(+)"    "MSX2_(+)"    "MXD4_(+)"    "MYEF2_(+)"   "NFIL3_(+)"  
##  [81] "NFYB_(+)"    "NHLH1_(+)"   "NKX2-1_(+)"  "NKX3-1_(+)"  "NR1I2_(+)"  
##  [86] "NR4A1_(+)"   "NRF1_(+)"    "ONECUT2_(+)" "OVOL2_(+)"   "PAX2_(+)"   
##  [91] "PAX7_(+)"    "PBX1_(+)"    "PDX1_(+)"    "PKNOX1_(+)"  "POU2F3_(+)" 
##  [96] "PRDM16_(+)"  "RARG_(+)"    "RBBP5_(+)"   "RELA_(+)"    "RFX5_(+)"   
## [101] "SIX2_(+)"    "SMC3_(+)"    "SOX13_(+)"   "SOX2_(+)"    "SP1_(+)"    
## [106] "SP2_(+)"     "SP4_(+)"     "SP7_(+)"     "SREBF2_(+)"  "STAT1_(+)"  
## [111] "STAT2_(+)"   "TAF7_(+)"    "TAGLN2_(+)"  "TAL1_(+)"    "TBP_(+)"    
## [116] "TBPL1_(+)"   "TBPL2_(+)"   "TBX15_(+)"   "TBX3_(+)"    "TCF7_(+)"   
## [121] "TET1_(+)"    "TFAP2A_(+)"  "TFE3_(+)"    "TFEB_(+)"    "TLX3_(+)"   
## [126] "TWIST1_(+)"  "UBTF_(+)"    "UQCRB_(+)"   "VSX1_(+)"    "WT1_(+)"    
## [131] "ZEB1_(+)"    "ZFHX2_(+)"   "ZFY_(+)"     "ZNF160_(+)"  "ZNF471_(+)" 
## [136] "ZNF502_(+)"  "ZNF560_(+)"  "ZNF580_(+)"  "ZNF768_(+)"  "ZNF773_(+)" 
## [141] "ZXDC_(+)"   
## 
## $human_IFNB_treated_NHBE
##  [1] "ATF3_(+)"    "BACH2_(+)"   "ELF3_(+)"    "ETV6_(+)"    "ETV7_(+)"   
##  [6] "FOXA1_(+)"   "FOXK1_(+)"   "GATA2_(+)"   "GCM1_(+)"    "GTF2B_(+)"  
## [11] "HIVEP2_(+)"  "HLX_(+)"     "HOXD11_(+)"  "IRF1_(+)"    "IRF2_(+)"   
## [16] "IRF7_(+)"    "IRF8_(+)"    "IRF9_(+)"    "NFIL3_(+)"   "NFIX_(+)"   
## [21] "NKX3-1_(+)"  "POU5F1B_(+)" "PRDM16_(+)"  "RARA_(+)"    "RELA_(+)"   
## [26] "RXRB_(+)"    "SOX11_(+)"   "SOX9_(+)"    "STAT2_(+)"   "TFEB_(+)"   
## [31] "VEZF1_(+)"
# Load and tidy data: adjusted pvalues, format
paste0("using pvalues from test : ", params$adj_pvals_mwu.fn)
## [1] "using pvalues from test : pvalues-mwu-2t-adjusted.csv"
pvalues <- as.data.frame(read_csv(paste0(params$inputdir,params$adj_pvals_mwu.fn), col_names = T))
if(params$celllines==1){
  names(pvalues) <- str_replace_all(names(pvalues), "-", "")
  names(pvalues) <- str_replace(names(pvalues), "w_vector_expressing_", "")
  names(pvalues) <- str_replace(names(pvalues), "1hr_Ruxolitinib_pretreatment", "pt")
}
rownames(pvalues) <- tfs

## Graph a Volcano Plot per condition
plots <- volcanos_per_exp(pvalues = pvalues, tfs_da = tfs_da,
                          test = "2t", save_png=T, outdir = params$outdir)
## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"
plots
## [[1]]
## NULL
## 
## [[2]]
## NULL
## 
## [[3]]
## NULL
## 
## [[4]]
## NULL
## 
## [[5]]
## NULL
## 
## [[6]]
## NULL
## 
## [[7]]
## NULL
## 
## [[8]]
## NULL
## 
## [[9]]
## NULL
## 
## [[10]]
## NULL
## 
## [[11]]
## NULL
## 
## $HPIV3_infected_A549

## 
## $IAV_infected_A549

## 
## $IAV_infected_NHBE

## 
## $IAVdNS1_infected_NHBE

## 
## $RSV_infected_A549

## 
## $SARSCoV2_infected_A549

## 
## $SARSCoV2_infected_A549_hACE2

## 
## $SARSCoV2_infected_A549_hACE2_pt

## 
## $SARSCoV2_infected_Calu3

## 
## $SARSCoV2_infected_NHBE

## 
## $human_IFNB_treated_NHBE

############################################
## Make lists of up/down regulons
tfs_da_up = list()
tfs_da_down = list()
for (exp in names(tfs_da)) {
  tfs_da_up[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in%  rownames(l2fc[exp] > 0)]
  tfs_da_down[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in% rownames(l2fc[exp] > 0)]
}

tfs_da_up
## $HPIV3_infected_A549
##   [1] "ALX3_(+)"    "ALX4_(+)"    "ARNT_(+)"    "ARNTL_(+)"   "ATF1_(+)"   
##   [6] "ATF4_(+)"    "ATF5_(+)"    "BCL6B_(+)"   "BHLHE40_(+)" "BHLHE41_(+)"
##  [11] "BRF1_(+)"    "CDX1_(+)"    "CHD2_(+)"    "CLOCK_(+)"   "CPEB1_(+)"  
##  [16] "CREB1_(+)"   "CREB5_(+)"   "DDIT3_(+)"   "DLX2_(+)"    "E2F1_(+)"   
##  [21] "E4F1_(+)"    "ELF2_(+)"    "ESRRA_(+)"   "FOSL1_(+)"   "FOXA2_(+)"  
##  [26] "FOXB1_(+)"   "FOXC2_(+)"   "FOXF2_(+)"   "FOXK1_(+)"   "FOXO1_(+)"  
##  [31] "FOXO3_(+)"   "FOXP2_(+)"   "GABPB1_(+)"  "GCM1_(+)"    "HAND1_(+)"  
##  [36] "HES6_(+)"    "HEY1_(+)"    "HEY2_(+)"    "HIVEP2_(+)"  "HLF_(+)"    
##  [41] "HOXA9_(+)"   "HOXB2_(+)"   "HOXB6_(+)"   "HOXB8_(+)"   "HOXB9_(+)"  
##  [46] "HOXC10_(+)"  "HOXC13_(+)"  "HOXC8_(+)"   "HOXD11_(+)"  "HSF2_(+)"   
##  [51] "IKZF2_(+)"   "IRF4_(+)"    "ISL2_(+)"    "KDM5A_(+)"   "KLF3_(+)"   
##  [56] "KLF7_(+)"    "KLF9_(+)"    "LHX4_(+)"    "MAF_(+)"     "MAZ_(+)"    
##  [61] "MECOM_(+)"   "MXD3_(+)"    "MXI1_(+)"    "MYCN_(+)"    "MYEF2_(+)"  
##  [66] "NEUROD1_(+)" "NFE2L1_(+)"  "NFIA_(+)"    "NFIL3_(+)"   "NFKB1_(+)"  
##  [71] "NFKB2_(+)"   "NFYA_(+)"    "NFYC_(+)"    "NHLH1_(+)"   "NKX3-1_(+)" 
##  [76] "NR2C1_(+)"   "NR5A2_(+)"   "OTP_(+)"     "PAX7_(+)"    "POU3F2_(+)" 
##  [81] "POU5F1_(+)"  "RARB_(+)"    "RFX2_(+)"    "RFX3_(+)"    "RREB1_(+)"  
##  [86] "RUNX2_(+)"   "SNAI3_(+)"   "SOX1_(+)"    "SOX15_(+)"   "SP6_(+)"    
##  [91] "TAF7_(+)"    "TAGLN2_(+)"  "TAL1_(+)"    "TBX15_(+)"   "TBX20_(+)"  
##  [96] "TCF3_(+)"    "TFE3_(+)"    "TFEB_(+)"    "THAP1_(+)"   "VSX1_(+)"   
## [101] "ZBTB33_(+)"  "ZBTB7A_(+)"  "ZEB1_(+)"    "ZFX_(+)"     "ZIC2_(+)"   
## [106] "ZNF134_(+)"  "ZNF143_(+)"  "ZNF148_(+)"  "ZNF160_(+)"  "ZNF227_(+)" 
## [111] "ZNF354C_(+)" "ZNF429_(+)"  "ZNF449_(+)"  "ZNF502_(+)"  "ZNF524_(+)" 
## [116] "ZNF571_(+)"  "ZNF597_(+)"  "ZNF607_(+)"  "ZNF668_(+)"  "ZNF672_(+)" 
## [121] "ZNF787_(+)"  "ZNF841_(+)"  "ZSCAN26_(+)"
## 
## $IAV_infected_A549
##   [1] "ALX1_(+)"     "ALX4_(+)"     "ARNT_(+)"     "ARNT2_(+)"    "ARNTL2_(+)"  
##   [6] "ASCL2_(+)"    "ATF2_(+)"     "ATF4_(+)"     "BACH1_(+)"    "BATF_(+)"    
##  [11] "BBX_(+)"      "BCL11A_(+)"   "BCL11B_(+)"   "BCLAF1_(+)"   "BHLHE40_(+)" 
##  [16] "BRF1_(+)"     "CDX2_(+)"     "CLOCK_(+)"    "CPEB1_(+)"    "CREB5_(+)"   
##  [21] "CTCFL_(+)"    "DLX3_(+)"     "DLX5_(+)"     "E2F1_(+)"     "E2F2_(+)"    
##  [26] "E2F4_(+)"     "E2F5_(+)"     "E2F6_(+)"     "E2F8_(+)"     "EGR1_(+)"    
##  [31] "EGR3_(+)"     "EHF_(+)"      "ELF1_(+)"     "ELF4_(+)"     "ELF5_(+)"    
##  [36] "ELK3_(+)"     "ELK4_(+)"     "EN1_(+)"      "EN2_(+)"      "ERF_(+)"     
##  [41] "ESRRA_(+)"    "ETS1_(+)"     "ETS2_(+)"     "ETV1_(+)"     "ETV7_(+)"    
##  [46] "FOSB_(+)"     "FOSL2_(+)"    "FOXB1_(+)"    "FOXC1_(+)"    "FOXD3_(+)"   
##  [51] "FOXF2_(+)"    "FOXM1_(+)"    "FOXO1_(+)"    "GABPA_(+)"    "GABPB1_(+)"  
##  [56] "GATA5_(+)"    "GCM1_(+)"     "GLI1_(+)"     "GLIS2_(+)"    "GRHL1_(+)"   
##  [61] "GRHL3_(+)"    "GRHPR_(+)"    "GSC_(+)"      "GSX2_(+)"     "GTF2B_(+)"   
##  [66] "GTF2IRD1_(+)" "HES1_(+)"     "HES5_(+)"     "HES6_(+)"     "HIC1_(+)"    
##  [71] "HINFP_(+)"    "HIVEP2_(+)"   "HLX_(+)"      "HNF1A_(+)"    "HNF1B_(+)"   
##  [76] "HOXA1_(+)"    "HOXA2_(+)"    "HOXA5_(+)"    "HOXA6_(+)"    "HOXA7_(+)"   
##  [81] "HOXA9_(+)"    "HOXB13_(+)"   "HOXB5_(+)"    "HOXB7_(+)"    "HOXB8_(+)"   
##  [86] "HOXC10_(+)"   "HOXC11_(+)"   "HOXC13_(+)"   "HOXC5_(+)"    "HOXC6_(+)"   
##  [91] "HOXD3_(+)"    "HOXD4_(+)"    "HOXD9_(+)"    "HTATIP2_(+)"  "IRF1_(+)"    
##  [96] "IRF2_(+)"     "IRF3_(+)"     "IRF5_(+)"     "IRF6_(+)"     "IRF7_(+)"    
## [101] "IRF9_(+)"     "IRX1_(+)"     "IRX2_(+)"     "IRX4_(+)"     "IRX5_(+)"    
## [106] "JUND_(+)"     "KLF10_(+)"    "KLF3_(+)"     "KLF4_(+)"     "KLF5_(+)"    
## [111] "KLF6_(+)"     "KLF8_(+)"     "KLF9_(+)"     "LBX2_(+)"     "LHX2_(+)"    
## [116] "LHX5_(+)"     "LMX1B_(+)"    "MAFA_(+)"     "MAFB_(+)"     "MAFG_(+)"    
## [121] "MAX_(+)"      "MAZ_(+)"      "MECOM_(+)"    "MEOX1_(+)"    "MNX1_(+)"    
## [126] "MSX2_(+)"     "MTF1_(+)"     "MXD1_(+)"     "MXD3_(+)"     "MXD4_(+)"    
## [131] "MXI1_(+)"     "MYCN_(+)"     "MYEF2_(+)"    "MYPOP_(+)"    "MZF1_(+)"    
## [136] "NEUROD1_(+)"  "NFATC4_(+)"   "NFE2_(+)"     "NFE2L1_(+)"   "NFIA_(+)"    
## [141] "NFKB1_(+)"    "NFYA_(+)"     "NFYC_(+)"     "NHLH2_(+)"    "NKX2-1_(+)"  
## [146] "NKX3-1_(+)"   "NR1H3_(+)"    "NR1H4_(+)"    "NR2E1_(+)"    "NR2F1_(+)"   
## [151] "NR2F6_(+)"    "ONECUT2_(+)"  "OTP_(+)"      "OTX1_(+)"     "OVOL2_(+)"   
## [156] "PAX7_(+)"     "PAX9_(+)"     "PHF21A_(+)"   "PHF8_(+)"     "PKNOX1_(+)"  
## [161] "POLE4_(+)"    "POLR2A_(+)"   "POLR3A_(+)"   "POLR3G_(+)"   "POU2F1_(+)"  
## [166] "POU2F3_(+)"   "POU3F1_(+)"   "POU3F4_(+)"   "PPARD_(+)"    "PRDM1_(+)"   
## [171] "PRDM15_(+)"   "PRRX2_(+)"    "PSMD12_(+)"   "RAB18_(+)"    "RARG_(+)"    
## [176] "REL_(+)"      "RFX2_(+)"     "RORA_(+)"     "RREB1_(+)"    "RXRG_(+)"    
## [181] "SATB1_(+)"    "SETDB1_(+)"   "SIN3A_(+)"    "SIX2_(+)"     "SIX5_(+)"    
## [186] "SMAD1_(+)"    "SMARCA5_(+)"  "SMARCC2_(+)"  "SNAI2_(+)"    "SNAI3_(+)"   
## [191] "SOX5_(+)"     "SP3_(+)"      "SP5_(+)"      "STAT1_(+)"    "STAT2_(+)"   
## [196] "STAT5A_(+)"   "STAT5B_(+)"   "TAGLN2_(+)"   "TBPL2_(+)"    "TCF12_(+)"   
## [201] "TCF3_(+)"     "TCF7_(+)"     "TEAD4_(+)"    "TEF_(+)"      "TFAP2A_(+)"  
## [206] "TFAP2C_(+)"   "TFAP2E_(+)"   "TFDP2_(+)"    "TGIF2_(+)"    "TLX2_(+)"    
## [211] "TRIM28_(+)"   "USF1_(+)"     "USF2_(+)"     "VAX1_(+)"     "VDR_(+)"     
## [216] "VSX2_(+)"     "ZBTB7A_(+)"   "ZFX_(+)"      "ZNF134_(+)"   "ZNF143_(+)"  
## [221] "ZNF208_(+)"   "ZNF219_(+)"   "ZNF274_(+)"   "ZNF281_(+)"   "ZNF35_(+)"   
## [226] "ZNF354C_(+)"  "ZNF426_(+)"   "ZNF429_(+)"   "ZNF471_(+)"   "ZNF483_(+)"  
## [231] "ZNF502_(+)"   "ZNF524_(+)"   "ZNF554_(+)"   "ZNF560_(+)"   "ZNF597_(+)"  
## [236] "ZNF672_(+)"   "ZNF682_(+)"   "ZNF720_(+)"   "ZNF729_(+)"   "ZNF730_(+)"  
## [241] "ZNF761_(+)"   "ZNF773_(+)"   "ZNF787_(+)"  
## 
## $IAV_infected_NHBE
##   [1] "AHCTF1_(+)"       "AIRE_(+)"         "ALX1_(+)"        
##   [4] "ALX3_(+)"         "ALX4_(+)"         "AR_(+)"          
##   [7] "ARID5B_(+)"       "ARNT_(+)"         "ARNTL2_(+)"      
##  [10] "ATF1_(+)"         "ATF3_(+)"         "BACH2_(+)"       
##  [13] "BATF_(+)"         "BCL3_(+)"         "BCLAF1_(+)"      
##  [16] "BDP1_(+)"         "BHLHE41_(+)"      "BNC2_(+)"        
##  [19] "BORCS8-MEF2B_(+)" "BRF1_(+)"         "CCNT2_(+)"       
##  [22] "CDX2_(+)"         "CEBPA_(+)"        "CEBPB_(+)"       
##  [25] "CEBPD_(+)"        "CELF6_(+)"        "CHD2_(+)"        
##  [28] "CKMT1B_(+)"       "CLOCK_(+)"        "CNOT3_(+)"       
##  [31] "CPEB1_(+)"        "CPSF4_(+)"        "CREB1_(+)"       
##  [34] "CREB3_(+)"        "CREB3L1_(+)"      "CUX1_(+)"        
##  [37] "DBX1_(+)"         "DLX2_(+)"         "DLX4_(+)"        
##  [40] "DMRT1_(+)"        "DMRTA1_(+)"       "DUXA_(+)"        
##  [43] "E2F3_(+)"         "E2F4_(+)"         "E2F6_(+)"        
##  [46] "EGR1_(+)"         "EGR2_(+)"         "EGR3_(+)"        
##  [49] "ELK3_(+)"         "EMX1_(+)"         "EN1_(+)"         
##  [52] "EN2_(+)"          "ENO1_(+)"         "EP300_(+)"       
##  [55] "ERF_(+)"          "ESRRA_(+)"        "ESRRB_(+)"       
##  [58] "ETV1_(+)"         "ETV3_(+)"         "ETV5_(+)"        
##  [61] "EVX2_(+)"         "FGF19_(+)"        "FOS_(+)"         
##  [64] "FOSL1_(+)"        "FOXA1_(+)"        "FOXA2_(+)"       
##  [67] "FOXB1_(+)"        "FOXC1_(+)"        "FOXC2_(+)"       
##  [70] "FOXD2_(+)"        "FOXD3_(+)"        "FOXD4_(+)"       
##  [73] "FOXD4L6_(+)"      "FOXF2_(+)"        "FOXJ2_(+)"       
##  [76] "FOXK1_(+)"        "FOXK2_(+)"        "FOXM1_(+)"       
##  [79] "FOXN1_(+)"        "FOXO1_(+)"        "FOXO3_(+)"       
##  [82] "FOXO6_(+)"        "FOXQ1_(+)"        "GATA3_(+)"       
##  [85] "GCM1_(+)"         "GLIS2_(+)"        "GMEB1_(+)"       
##  [88] "GRHL2_(+)"        "GTF2IRD1_(+)"     "HAND1_(+)"       
##  [91] "HDAC1_(+)"        "HES5_(+)"         "HEY1_(+)"        
##  [94] "HINFP_(+)"        "HLF_(+)"          "HMGB1_(+)"       
##  [97] "HNF1A_(+)"        "HNF1B_(+)"        "HOXA10_(+)"      
## [100] "HOXA2_(+)"        "HOXA5_(+)"        "HOXA9_(+)"       
## [103] "HOXB13_(+)"       "HOXB4_(+)"        "HOXB6_(+)"       
## [106] "HOXB8_(+)"        "HOXB9_(+)"        "HOXC10_(+)"      
## [109] "HOXC13_(+)"       "HOXC4_(+)"        "HOXC6_(+)"       
## [112] "HOXC8_(+)"        "HOXC9_(+)"        "HOXD11_(+)"      
## [115] "HOXD13_(+)"       "HOXD3_(+)"        "HOXD4_(+)"       
## [118] "HSF2_(+)"         "HSF4_(+)"         "HTATIP2_(+)"     
## [121] "IKZF3_(+)"        "ING3_(+)"         "IRF1_(+)"        
## [124] "IRF4_(+)"         "IRX2_(+)"         "IRX5_(+)"        
## [127] "ISL2_(+)"         "JUN_(+)"          "JUNB_(+)"        
## [130] "JUND_(+)"         "KDM5A_(+)"        "KLF1_(+)"        
## [133] "KLF10_(+)"        "KLF11_(+)"        "KLF12_(+)"       
## [136] "KLF13_(+)"        "KLF14_(+)"        "KLF2_(+)"        
## [139] "KLF5_(+)"         "KLF8_(+)"         "LHX4_(+)"        
## [142] "LHX8_(+)"         "LHX9_(+)"         "LMX1B_(+)"       
## [145] "MAF_(+)"          "MAFB_(+)"         "MAFF_(+)"        
## [148] "MAFG_(+)"         "MEF2B_(+)"        "MEF2C_(+)"       
## [151] "MEOX2_(+)"        "MLXIP_(+)"        "MLXIPL_(+)"      
## [154] "MNT_(+)"          "MNX1_(+)"         "MSX1_(+)"        
## [157] "MSX2_(+)"         "MYEF2_(+)"        "MYOD1_(+)"       
## [160] "MZF1_(+)"         "NFATC2_(+)"       "NFE2L2_(+)"      
## [163] "NFE2L3_(+)"       "NFIA_(+)"         "NFIB_(+)"        
## [166] "NFIC_(+)"         "NFIL3_(+)"        "NFKB2_(+)"       
## [169] "NHLH1_(+)"        "NKX2-1_(+)"       "NKX2-5_(+)"      
## [172] "NKX3-1_(+)"       "NPDC1_(+)"        "NR0B1_(+)"       
## [175] "NR1D1_(+)"        "NR2E1_(+)"        "NR2F1_(+)"       
## [178] "NR3C1_(+)"        "NR4A1_(+)"        "NR5A2_(+)"       
## [181] "NR6A1_(+)"        "NRF1_(+)"         "ONECUT1_(+)"     
## [184] "ONECUT2_(+)"      "ONECUT3_(+)"      "OTP_(+)"         
## [187] "PATZ1_(+)"        "PAX7_(+)"         "PDX1_(+)"        
## [190] "PKNOX1_(+)"       "POLE3_(+)"        "POLR2A_(+)"      
## [193] "POLR3G_(+)"       "POU3F2_(+)"       "POU3F4_(+)"      
## [196] "POU5F1_(+)"       "PPARD_(+)"        "PROX1_(+)"       
## [199] "PRRX1_(+)"        "PSMD12_(+)"       "RARB_(+)"        
## [202] "RARG_(+)"         "RBBP5_(+)"        "REL_(+)"         
## [205] "RELA_(+)"         "RFX1_(+)"         "RFX2_(+)"        
## [208] "RFX3_(+)"         "RFX5_(+)"         "RFXAP_(+)"       
## [211] "SATB1_(+)"        "SIN3A_(+)"        "SIX2_(+)"        
## [214] "SIX4_(+)"         "SIX5_(+)"         "SOHLH2_(+)"      
## [217] "SOX1_(+)"         "SOX13_(+)"        "SOX15_(+)"       
## [220] "SOX2_(+)"         "SOX21_(+)"        "SOX4_(+)"        
## [223] "SOX6_(+)"         "SP7_(+)"          "SP9_(+)"         
## [226] "SPDEF_(+)"        "SREBF2_(+)"       "STAT4_(+)"       
## [229] "TAF7_(+)"         "TAGLN2_(+)"       "TAL1_(+)"        
## [232] "TBP_(+)"          "TBPL1_(+)"        "TBX15_(+)"       
## [235] "TBX20_(+)"        "TBX3_(+)"         "TBX6_(+)"        
## [238] "TCF4_(+)"         "TCF7_(+)"         "TET1_(+)"        
## [241] "TFAP2A_(+)"       "TFDP1_(+)"        "TFE3_(+)"        
## [244] "TFEB_(+)"         "THAP1_(+)"        "TLX2_(+)"        
## [247] "TLX3_(+)"         "TRPS1_(+)"        "UQCRB_(+)"       
## [250] "USF2_(+)"         "VEZF1_(+)"        "VSX1_(+)"        
## [253] "VSX2_(+)"         "XBP1_(+)"         "YBX1_(+)"        
## [256] "ZBTB41_(+)"       "ZBTB43_(+)"       "ZEB1_(+)"        
## [259] "ZFHX2_(+)"        "ZIC2_(+)"         "ZNF160_(+)"      
## [262] "ZNF189_(+)"       "ZNF208_(+)"       "ZNF239_(+)"      
## [265] "ZNF263_(+)"       "ZNF264_(+)"       "ZNF274_(+)"      
## [268] "ZNF281_(+)"       "ZNF316_(+)"       "ZNF441_(+)"      
## [271] "ZNF442_(+)"       "ZNF467_(+)"       "ZNF471_(+)"      
## [274] "ZNF486_(+)"       "ZNF502_(+)"       "ZNF513_(+)"      
## [277] "ZNF560_(+)"       "ZNF571_(+)"       "ZNF597_(+)"      
## [280] "ZNF668_(+)"       "ZNF713_(+)"       "ZNF721_(+)"      
## [283] "ZNF740_(+)"       "ZNF816_(+)"       "ZNF836_(+)"      
## [286] "ZSCAN31_(+)"      "ZXDC_(+)"        
## 
## $IAVdNS1_infected_NHBE
##   [1] "AIRE_(+)"     "ALX1_(+)"     "AR_(+)"       "ARNT_(+)"     "ARNTL2_(+)"  
##   [6] "ATF1_(+)"     "ATF3_(+)"     "ATF5_(+)"     "BACH2_(+)"    "BATF_(+)"    
##  [11] "BCL3_(+)"     "BCLAF1_(+)"   "BDP1_(+)"     "BHLHE40_(+)"  "BHLHE41_(+)" 
##  [16] "BNC2_(+)"     "BRF1_(+)"     "CCNT2_(+)"    "CDX2_(+)"     "CEBPA_(+)"   
##  [21] "CEBPB_(+)"    "CEBPD_(+)"    "CELF6_(+)"    "CHD2_(+)"     "CKMT1B_(+)"  
##  [26] "CNOT3_(+)"    "CPSF4_(+)"    "CREB1_(+)"    "CREB3_(+)"    "CREB3L1_(+)" 
##  [31] "CTCF_(+)"     "DBX1_(+)"     "DDIT3_(+)"    "DLX2_(+)"     "E2F3_(+)"    
##  [36] "E2F4_(+)"     "E2F6_(+)"     "E2F8_(+)"     "EGR1_(+)"     "EGR2_(+)"    
##  [41] "EGR3_(+)"     "ELK3_(+)"     "EMX1_(+)"     "EN2_(+)"      "ENO1_(+)"    
##  [46] "EP300_(+)"    "ERF_(+)"      "ESR2_(+)"     "ESRRA_(+)"    "ESRRB_(+)"   
##  [51] "ETV1_(+)"     "ETV3_(+)"     "ETV5_(+)"     "EVX2_(+)"     "FGF19_(+)"   
##  [56] "FOS_(+)"      "FOSL1_(+)"    "FOXA1_(+)"    "FOXA2_(+)"    "FOXB1_(+)"   
##  [61] "FOXC1_(+)"    "FOXC2_(+)"    "FOXD2_(+)"    "FOXD3_(+)"    "FOXD4_(+)"   
##  [66] "FOXD4L4_(+)"  "FOXD4L6_(+)"  "FOXK1_(+)"    "FOXK2_(+)"    "FOXM1_(+)"   
##  [71] "FOXO1_(+)"    "FOXO3_(+)"    "FOXO6_(+)"    "FOXQ1_(+)"    "GATA3_(+)"   
##  [76] "GATA6_(+)"    "GCM1_(+)"     "GMEB1_(+)"    "GMEB2_(+)"    "GPD1_(+)"    
##  [81] "GRHL2_(+)"    "GSX1_(+)"     "GTF2IRD1_(+)" "HAND1_(+)"    "HDAC1_(+)"   
##  [86] "HES5_(+)"     "HIC1_(+)"     "HINFP_(+)"    "HLF_(+)"      "HMGB1_(+)"   
##  [91] "HNF1B_(+)"    "HOXA10_(+)"   "HOXA2_(+)"    "HOXA5_(+)"    "HOXA9_(+)"   
##  [96] "HOXB13_(+)"   "HOXB2_(+)"    "HOXB6_(+)"    "HOXB8_(+)"    "HOXB9_(+)"   
## [101] "HOXC10_(+)"   "HOXC13_(+)"   "HOXC4_(+)"    "HOXC6_(+)"    "HOXC8_(+)"   
## [106] "HOXC9_(+)"    "HOXD11_(+)"   "HOXD13_(+)"   "HOXD3_(+)"    "HOXD4_(+)"   
## [111] "HSF2_(+)"     "HSF4_(+)"     "HTATIP2_(+)"  "IKZF3_(+)"    "ING3_(+)"    
## [116] "IRF1_(+)"     "IRF4_(+)"     "IRX2_(+)"     "IRX5_(+)"     "ISL2_(+)"    
## [121] "JUN_(+)"      "JUNB_(+)"     "JUND_(+)"     "KDM5A_(+)"    "KLF1_(+)"    
## [126] "KLF11_(+)"    "KLF12_(+)"    "KLF14_(+)"    "KLF2_(+)"     "KLF5_(+)"    
## [131] "KLF8_(+)"     "LHX4_(+)"     "LHX8_(+)"     "LHX9_(+)"     "MAF_(+)"     
## [136] "MAFB_(+)"     "MAFF_(+)"     "MAFG_(+)"     "MEF2B_(+)"    "MLXIP_(+)"   
## [141] "MLXIPL_(+)"   "MNT_(+)"      "MNX1_(+)"     "MSX1_(+)"     "MSX2_(+)"    
## [146] "MXD4_(+)"     "MXI1_(+)"     "MYEF2_(+)"    "MYOD1_(+)"    "MYPOP_(+)"   
## [151] "MZF1_(+)"     "NFATC2_(+)"   "NFE2L1_(+)"   "NFE2L2_(+)"   "NFIA_(+)"    
## [156] "NFIB_(+)"     "NFIC_(+)"     "NFIL3_(+)"    "NFKB2_(+)"    "NHLH1_(+)"   
## [161] "NHLH2_(+)"    "NKX2-1_(+)"   "NKX3-1_(+)"   "NPDC1_(+)"    "NR0B1_(+)"   
## [166] "NR1D1_(+)"    "NR2C1_(+)"    "NR2F1_(+)"    "NR4A1_(+)"    "NR5A2_(+)"   
## [171] "NR6A1_(+)"    "NRF1_(+)"     "ONECUT1_(+)"  "ONECUT2_(+)"  "ONECUT3_(+)" 
## [176] "OTP_(+)"      "PATZ1_(+)"    "PAX7_(+)"     "PHF21A_(+)"   "PKNOX1_(+)"  
## [181] "POLE3_(+)"    "POLR2A_(+)"   "POLR3A_(+)"   "POLR3G_(+)"   "POU1F1_(+)"  
## [186] "POU3F2_(+)"   "POU3F4_(+)"   "POU4F3_(+)"   "POU5F1_(+)"   "PPARD_(+)"   
## [191] "PROX1_(+)"    "PSMD12_(+)"   "RARB_(+)"     "RARG_(+)"     "RBBP5_(+)"   
## [196] "REL_(+)"      "RELA_(+)"     "RFX1_(+)"     "RFX2_(+)"     "RFX3_(+)"    
## [201] "RFX5_(+)"     "RFXAP_(+)"    "SHOX2_(+)"    "SIX4_(+)"     "SIX5_(+)"    
## [206] "SMAD3_(+)"    "SNAPC4_(+)"   "SOHLH2_(+)"   "SOX1_(+)"     "SOX13_(+)"   
## [211] "SOX15_(+)"    "SOX21_(+)"    "SOX4_(+)"     "SOX6_(+)"     "SP9_(+)"     
## [216] "SPDEF_(+)"    "SREBF2_(+)"   "STAT4_(+)"    "TAF7_(+)"     "TAGLN2_(+)"  
## [221] "TAL1_(+)"     "TBP_(+)"      "TBPL1_(+)"    "TBX18_(+)"    "TBX20_(+)"   
## [226] "TBX3_(+)"     "TCF4_(+)"     "TCF7_(+)"     "TEF_(+)"      "TET1_(+)"    
## [231] "TFAP2A_(+)"   "TFDP1_(+)"    "TFE3_(+)"     "TFEB_(+)"     "THAP1_(+)"   
## [236] "TLX3_(+)"     "TRPS1_(+)"    "UBP1_(+)"     "UBTF_(+)"     "UQCRB_(+)"   
## [241] "VEZF1_(+)"    "VSX1_(+)"     "VSX2_(+)"     "XBP1_(+)"     "YBX1_(+)"    
## [246] "YY2_(+)"      "ZBTB41_(+)"   "ZBTB43_(+)"   "ZDHHC15_(+)"  "ZEB1_(+)"    
## [251] "ZFHX2_(+)"    "ZFHX3_(+)"    "ZFP64_(+)"    "ZFX_(+)"      "ZIC2_(+)"    
## [256] "ZNF143_(+)"   "ZNF160_(+)"   "ZNF205_(+)"   "ZNF208_(+)"   "ZNF239_(+)"  
## [261] "ZNF25_(+)"    "ZNF263_(+)"   "ZNF264_(+)"   "ZNF274_(+)"   "ZNF281_(+)"  
## [266] "ZNF316_(+)"   "ZNF426_(+)"   "ZNF441_(+)"   "ZNF449_(+)"   "ZNF467_(+)"  
## [271] "ZNF471_(+)"   "ZNF483_(+)"   "ZNF486_(+)"   "ZNF502_(+)"   "ZNF513_(+)"  
## [276] "ZNF560_(+)"   "ZNF571_(+)"   "ZNF597_(+)"   "ZNF668_(+)"   "ZNF713_(+)"  
## [281] "ZNF717_(+)"   "ZNF721_(+)"   "ZNF740_(+)"   "ZNF816_(+)"   "ZNF841_(+)"  
## [286] "ZSCAN31_(+)"  "ZXDC_(+)"    
## 
## $RSV_infected_A549
##  [1] "ARNT_(+)"    "BCLAF1_(+)"  "BHLHE40_(+)" "CDX1_(+)"    "CLOCK_(+)"  
##  [6] "CREB5_(+)"   "ELF2_(+)"    "ELK3_(+)"    "EP300_(+)"   "ETV1_(+)"   
## [11] "ETV3_(+)"    "FOSL2_(+)"   "GMEB1_(+)"   "HEY1_(+)"    "HOXB6_(+)"  
## [16] "IRX2_(+)"    "KLF7_(+)"    "MAX_(+)"     "MNX1_(+)"    "MXD3_(+)"   
## [21] "MYCN_(+)"    "NFATC2_(+)"  "NFKB1_(+)"   "NFYA_(+)"    "NFYC_(+)"   
## [26] "NKX3-1_(+)"  "NR2F1_(+)"   "PKNOX1_(+)"  "POLR3A_(+)"  "POLR3G_(+)" 
## [31] "PPARD_(+)"   "PRDM16_(+)"  "REL_(+)"     "RREB1_(+)"   "SMAD1_(+)"  
## [36] "SNAI3_(+)"   "SP5_(+)"     "TCF7_(+)"    "ZFX_(+)"     "ZNF208_(+)" 
## [41] "ZNF264_(+)"  "ZNF267_(+)"  "ZNF426_(+)"  "ZNF429_(+)"  "ZNF502_(+)" 
## [46] "ZNF560_(+)"  "ZNF773_(+)" 
## 
## $SARSCoV2_infected_A549
##   [1] "ALX1_(+)"     "ALX3_(+)"     "ALX4_(+)"     "ARNT_(+)"     "ARNT2_(+)"   
##   [6] "ARNTL2_(+)"   "ATF2_(+)"     "ATF4_(+)"     "ATF6_(+)"     "BACH1_(+)"   
##  [11] "BBX_(+)"      "BCL11A_(+)"   "BCL11B_(+)"   "BCLAF1_(+)"   "BHLHA15_(+)" 
##  [16] "BHLHE40_(+)"  "BRF1_(+)"     "CDX2_(+)"     "CELF6_(+)"    "CLOCK_(+)"   
##  [21] "CPEB1_(+)"    "CTCFL_(+)"    "DLX3_(+)"     "DLX4_(+)"     "DLX5_(+)"    
##  [26] "DRGX_(+)"     "E2F1_(+)"     "E2F2_(+)"     "E2F4_(+)"     "E2F5_(+)"    
##  [31] "EHF_(+)"      "ELF1_(+)"     "ELK1_(+)"     "ELK3_(+)"     "ELK4_(+)"    
##  [36] "EN1_(+)"      "ERF_(+)"      "ETS1_(+)"     "ETS2_(+)"     "ETV1_(+)"    
##  [41] "ETV3_(+)"     "FEV_(+)"      "FLI1_(+)"     "FOSL2_(+)"    "FOXA3_(+)"   
##  [46] "FOXD2_(+)"    "FOXD3_(+)"    "FOXF2_(+)"    "FOXP4_(+)"    "FOXQ1_(+)"   
##  [51] "GABPA_(+)"    "GABPB1_(+)"   "GATA5_(+)"    "GCM1_(+)"     "GLI1_(+)"    
##  [56] "GLIS2_(+)"    "GRHL3_(+)"    "GRHPR_(+)"    "GSX2_(+)"     "GTF2B_(+)"   
##  [61] "GTF2IRD1_(+)" "GTF3A_(+)"    "HES5_(+)"     "HES6_(+)"     "HEY1_(+)"    
##  [66] "HIC1_(+)"     "HLX_(+)"      "HNF1A_(+)"    "HNF1B_(+)"    "HOXA1_(+)"   
##  [71] "HOXA6_(+)"    "HOXA7_(+)"    "HOXB13_(+)"   "HOXB2_(+)"    "HOXB5_(+)"   
##  [76] "HOXB6_(+)"    "HOXB8_(+)"    "HOXC10_(+)"   "HOXC11_(+)"   "HOXC6_(+)"   
##  [81] "HOXD3_(+)"    "HOXD4_(+)"    "HOXD9_(+)"    "HSF4_(+)"     "HTATIP2_(+)" 
##  [86] "IKZF2_(+)"    "ING3_(+)"     "IRF2_(+)"     "IRF6_(+)"     "IRF9_(+)"    
##  [91] "IRX1_(+)"     "IRX2_(+)"     "IRX4_(+)"     "JUND_(+)"     "KLF10_(+)"   
##  [96] "KLF6_(+)"     "KLF7_(+)"     "KLF8_(+)"     "LBX2_(+)"     "LHX2_(+)"    
## [101] "LMX1B_(+)"    "MAF_(+)"      "MAFA_(+)"     "MAX_(+)"      "MAZ_(+)"     
## [106] "MECOM_(+)"    "MEOX1_(+)"    "MESP1_(+)"    "MNX1_(+)"     "MXD1_(+)"    
## [111] "MXD3_(+)"     "MXI1_(+)"     "MYCN_(+)"     "MYOD1_(+)"    "MYPOP_(+)"   
## [116] "MZF1_(+)"     "NEUROD1_(+)"  "NFATC4_(+)"   "NFE2L1_(+)"   "NFIA_(+)"    
## [121] "NFIB_(+)"     "NFKB1_(+)"    "NFYA_(+)"     "NFYC_(+)"     "NHLH2_(+)"   
## [126] "NKX2-1_(+)"   "NKX2-5_(+)"   "NKX3-1_(+)"   "NR1H3_(+)"    "NR1H4_(+)"   
## [131] "NR2E1_(+)"    "NR2F1_(+)"    "NR2F6_(+)"    "NR6A1_(+)"    "ONECUT2_(+)" 
## [136] "OTP_(+)"      "OTX1_(+)"     "PATZ1_(+)"    "PAX7_(+)"     "PAX9_(+)"    
## [141] "PHF8_(+)"     "PKNOX1_(+)"   "POLE4_(+)"    "POLR2A_(+)"   "POLR3A_(+)"  
## [146] "POLR3G_(+)"   "POU3F4_(+)"   "PRDM1_(+)"    "PRDM15_(+)"   "PRRX2_(+)"   
## [151] "PSMD12_(+)"   "RAB18_(+)"    "RB1_(+)"      "RFX1_(+)"     "RFX2_(+)"    
## [156] "RREB1_(+)"    "RUNX2_(+)"    "RXRG_(+)"     "SATB1_(+)"    "SHOX2_(+)"   
## [161] "SIN3A_(+)"    "SIX5_(+)"     "SMAD1_(+)"    "SMARCA5_(+)"  "SMARCC2_(+)" 
## [166] "SNAI1_(+)"    "SNAI2_(+)"    "SNAI3_(+)"    "SOX5_(+)"     "SP3_(+)"     
## [171] "SP5_(+)"      "SPDEF_(+)"    "STAT1_(+)"    "STAT5B_(+)"   "TAL2_(+)"    
## [176] "TCF3_(+)"     "TCF7L1_(+)"   "TCF7L2_(+)"   "TEAD2_(+)"    "TFAP2A_(+)"  
## [181] "TFAP2C_(+)"   "TFDP2_(+)"    "THRA_(+)"     "TLX1_(+)"     "TLX2_(+)"    
## [186] "TRIM28_(+)"   "USF1_(+)"     "USF2_(+)"     "VAX1_(+)"     "VSX2_(+)"    
## [191] "ZFHX3_(+)"    "ZFP64_(+)"    "ZFX_(+)"      "ZIC2_(+)"     "ZNF134_(+)"  
## [196] "ZNF143_(+)"   "ZNF219_(+)"   "ZNF267_(+)"   "ZNF281_(+)"   "ZNF319_(+)"  
## [201] "ZNF35_(+)"    "ZNF354C_(+)"  "ZNF426_(+)"   "ZNF429_(+)"   "ZNF471_(+)"  
## [206] "ZNF483_(+)"   "ZNF486_(+)"   "ZNF502_(+)"   "ZNF513_(+)"   "ZNF524_(+)"  
## [211] "ZNF554_(+)"   "ZNF560_(+)"   "ZNF583_(+)"   "ZNF597_(+)"   "ZNF672_(+)"  
## [216] "ZNF720_(+)"   "ZNF729_(+)"   "ZNF730_(+)"   "ZNF75A_(+)"   "ZNF768_(+)"  
## [221] "ZNF773_(+)"   "ZNF787_(+)"  
## 
## $SARSCoV2_infected_A549_hACE2
##  [1] "ATF3_(+)"    "CEBPD_(+)"   "DLX2_(+)"    "EGR3_(+)"    "EMX1_(+)"   
##  [6] "ETV6_(+)"    "ETV7_(+)"    "FOXK1_(+)"   "HIVEP2_(+)"  "HOXB6_(+)"  
## [11] "IRF1_(+)"    "IRF5_(+)"    "IRF8_(+)"    "IRF9_(+)"    "KLF13_(+)"  
## [16] "MEF2B_(+)"   "NEUROD2_(+)" "NFE2L2_(+)"  "NKX3-1_(+)"  "RXRG_(+)"   
## [21] "SMARCA5_(+)" "SOX2_(+)"    "SOX21_(+)"   "STAT1_(+)"   "STAT2_(+)"  
## [26] "TP53_(+)"    "TP73_(+)"    "XBP1_(+)"    "ZNF768_(+)" 
## 
## $SARSCoV2_infected_A549_hACE2_pt
##   [1] "AIRE_(+)"    "AKR1A1_(+)"  "ALX4_(+)"    "ARID5B_(+)"  "ARNT_(+)"   
##   [6] "ATF3_(+)"    "BCLAF1_(+)"  "BHLHA15_(+)" "BHLHE40_(+)" "BRF2_(+)"   
##  [11] "CDX2_(+)"    "CEBPA_(+)"   "CEBPD_(+)"   "CLOCK_(+)"   "CTCFL_(+)"  
##  [16] "DLX2_(+)"    "DLX3_(+)"    "DLX4_(+)"    "DMRT1_(+)"   "DMRTA1_(+)" 
##  [21] "E2F1_(+)"    "E2F2_(+)"    "E2F7_(+)"    "E2F8_(+)"    "EBF1_(+)"   
##  [26] "EGR1_(+)"    "EHF_(+)"     "ELF1_(+)"    "ELF4_(+)"    "ELK3_(+)"   
##  [31] "ELK4_(+)"    "EMX1_(+)"    "ENO1_(+)"    "ERF_(+)"     "ETS1_(+)"   
##  [36] "ETS2_(+)"    "ETV6_(+)"    "ETV7_(+)"    "FOSB_(+)"    "FOSL2_(+)"  
##  [41] "FOXB1_(+)"   "FOXD3_(+)"   "FOXK1_(+)"   "FOXK2_(+)"   "FOXM1_(+)"  
##  [46] "FOXN1_(+)"   "FOXO1_(+)"   "FOXP1_(+)"   "GATA5_(+)"   "GLI1_(+)"   
##  [51] "GRHPR_(+)"   "GSC2_(+)"    "GTF2B_(+)"   "HES6_(+)"    "HEY1_(+)"   
##  [56] "HIVEP2_(+)"  "HLX_(+)"     "HNF4G_(+)"   "HOXA2_(+)"   "HOXA6_(+)"  
##  [61] "HOXA9_(+)"   "HOXB1_(+)"   "HOXB6_(+)"   "HOXC11_(+)"  "HOXC5_(+)"  
##  [66] "HOXC9_(+)"   "HOXD4_(+)"   "HSF1_(+)"    "IKZF2_(+)"   "IRF1_(+)"   
##  [71] "IRF2_(+)"    "IRF5_(+)"    "IRF6_(+)"    "IRF7_(+)"    "IRF8_(+)"   
##  [76] "IRF9_(+)"    "IRX5_(+)"    "JUND_(+)"    "KDM4D_(+)"   "KLF13_(+)"  
##  [81] "KLF5_(+)"    "KLF6_(+)"    "KLF7_(+)"    "LHX1_(+)"    "LHX2_(+)"   
##  [86] "LMX1B_(+)"   "MAFB_(+)"    "MAX_(+)"     "MAZ_(+)"     "MLXIP_(+)"  
##  [91] "MLXIPL_(+)"  "MNX1_(+)"    "MXD3_(+)"    "MYCN_(+)"    "MYEF2_(+)"  
##  [96] "MZF1_(+)"    "NEUROD2_(+)" "NFATC2_(+)"  "NFE2L1_(+)"  "NFE2L2_(+)" 
## [101] "NFKB1_(+)"   "NKX2-2_(+)"  "NKX3-1_(+)"  "NPDC1_(+)"   "NR1D1_(+)"  
## [106] "NR1H3_(+)"   "NR1H4_(+)"   "NR2F1_(+)"   "NR2F6_(+)"   "NR3C2_(+)"  
## [111] "NR4A1_(+)"   "ONECUT2_(+)" "PBX3_(+)"    "PDX1_(+)"    "PHF21A_(+)" 
## [116] "POLE4_(+)"   "POLR3A_(+)"  "POLR3G_(+)"  "POU2F3_(+)"  "POU3F1_(+)" 
## [121] "POU3F4_(+)"  "PPARD_(+)"   "PRDM16_(+)"  "PRRX1_(+)"   "PRRX2_(+)"  
## [126] "REL_(+)"     "RFX1_(+)"    "RFXAP_(+)"   "RUNX2_(+)"   "RXRG_(+)"   
## [131] "SATB1_(+)"   "SETDB1_(+)"  "SHOX2_(+)"   "SIX2_(+)"    "SIX5_(+)"   
## [136] "SMARCA5_(+)" "SMARCC2_(+)" "SNAI3_(+)"   "SOX2_(+)"    "SOX21_(+)"  
## [141] "SOX9_(+)"    "SP6_(+)"     "SREBF1_(+)"  "STAT1_(+)"   "STAT2_(+)"  
## [146] "STAT5B_(+)"  "TAF1_(+)"    "TBX20_(+)"   "TBX3_(+)"    "TCF12_(+)"  
## [151] "TEAD2_(+)"   "TET1_(+)"    "TFAP2A_(+)"  "TFAP2C_(+)"  "TGIF1_(+)"  
## [156] "TP73_(+)"    "TRIM28_(+)"  "TWIST1_(+)"  "USF1_(+)"    "VAX1_(+)"   
## [161] "VEZF1_(+)"   "XBP1_(+)"    "ZBED1_(+)"   "ZBTB41_(+)"  "ZFHX3_(+)"  
## [166] "ZFX_(+)"     "ZNF239_(+)"  "ZNF274_(+)"  "ZNF276_(+)"  "ZNF460_(+)" 
## [171] "ZNF502_(+)"  "ZNF524_(+)"  "ZNF579_(+)"  "ZNF583_(+)"  "ZNF652_(+)" 
## [176] "ZNF668_(+)"  "ZNF672_(+)"  "ZNF701_(+)"  "ZNF721_(+)"  "ZNF730_(+)" 
## [181] "ZNF768_(+)"  "ZNF773_(+)"  "ZNF787_(+)"  "ZXDC_(+)"   
## 
## $SARSCoV2_infected_Calu3
##   [1] "AKR1A1_(+)"       "ALX4_(+)"         "AR_(+)"          
##   [4] "ARID3C_(+)"       "ARID5B_(+)"       "ARNT_(+)"        
##   [7] "ARNT2_(+)"        "ARNTL_(+)"        "ARNTL2_(+)"      
##  [10] "ARX_(+)"          "ASCL1_(+)"        "ASCL2_(+)"       
##  [13] "ATF3_(+)"         "ATF4_(+)"         "ATF6_(+)"        
##  [16] "ATF6B_(+)"        "BACH2_(+)"        "BATF_(+)"        
##  [19] "BBX_(+)"          "BCL11A_(+)"       "BCL3_(+)"        
##  [22] "BDP1_(+)"         "BHLHE40_(+)"      "BHLHE41_(+)"     
##  [25] "BNC2_(+)"         "BORCS8-MEF2B_(+)" "BRCA1_(+)"       
##  [28] "BRF2_(+)"         "CCNT2_(+)"        "CDX2_(+)"        
##  [31] "CEBPD_(+)"        "CEBPG_(+)"        "CIC_(+)"         
##  [34] "CPEB1_(+)"        "CREB3L1_(+)"      "CREB5_(+)"       
##  [37] "CREBL2_(+)"       "CTCF_(+)"         "CUX1_(+)"        
##  [40] "DBP_(+)"          "DDIT3_(+)"        "DLX2_(+)"        
##  [43] "DLX3_(+)"         "DLX4_(+)"         "DMRT1_(+)"       
##  [46] "DRGX_(+)"         "DUX4_(+)"         "DUXA_(+)"        
##  [49] "E2F1_(+)"         "E2F2_(+)"         "E2F8_(+)"        
##  [52] "E4F1_(+)"         "EGR2_(+)"         "EGR3_(+)"        
##  [55] "EHF_(+)"          "ELF1_(+)"         "ELF4_(+)"        
##  [58] "ELK1_(+)"         "ELK3_(+)"         "ELK4_(+)"        
##  [61] "EMX1_(+)"         "ENO1_(+)"         "EOMES_(+)"       
##  [64] "EP300_(+)"        "ESRRA_(+)"        "ESX1_(+)"        
##  [67] "ETS1_(+)"         "ETS2_(+)"         "ETV3_(+)"        
##  [70] "ETV4_(+)"         "ETV6_(+)"         "ETV7_(+)"        
##  [73] "EVX2_(+)"         "FBXL19_(+)"       "FEV_(+)"         
##  [76] "FOSB_(+)"         "FOSL1_(+)"        "FOSL2_(+)"       
##  [79] "FOXA2_(+)"        "FOXA3_(+)"        "FOXC1_(+)"       
##  [82] "FOXC2_(+)"        "FOXD2_(+)"        "FOXD3_(+)"       
##  [85] "FOXD4L6_(+)"      "FOXF1_(+)"        "FOXF2_(+)"       
##  [88] "FOXG1_(+)"        "FOXJ2_(+)"        "FOXJ3_(+)"       
##  [91] "FOXK1_(+)"        "FOXL1_(+)"        "FOXM1_(+)"       
##  [94] "FOXN1_(+)"        "FOXO1_(+)"        "FOXO3_(+)"       
##  [97] "FOXO4_(+)"        "GABPB1_(+)"       "GATA2_(+)"       
## [100] "GATA3_(+)"        "GATA5_(+)"        "GATA6_(+)"       
## [103] "GBX1_(+)"         "GLI1_(+)"         "GLIS2_(+)"       
## [106] "GMEB1_(+)"        "GMEB2_(+)"        "GRHL1_(+)"       
## [109] "GRHL2_(+)"        "GRHPR_(+)"        "GSC_(+)"         
## [112] "GSC2_(+)"         "GTF2B_(+)"        "GTF2IRD1_(+)"    
## [115] "GTF3A_(+)"        "HAND1_(+)"        "HDAC2_(+)"       
## [118] "HES1_(+)"         "HES5_(+)"         "HES6_(+)"        
## [121] "HESX1_(+)"        "HEY2_(+)"         "HINFP_(+)"       
## [124] "HIVEP1_(+)"       "HIVEP2_(+)"       "HLF_(+)"         
## [127] "HLX_(+)"          "HMGB1_(+)"        "HNF1A_(+)"       
## [130] "HOXA2_(+)"        "HOXA6_(+)"        "HOXA9_(+)"       
## [133] "HOXB4_(+)"        "HOXB6_(+)"        "HOXB7_(+)"       
## [136] "HOXB8_(+)"        "HOXB9_(+)"        "HOXC10_(+)"      
## [139] "HOXC11_(+)"       "HOXC13_(+)"       "HOXC4_(+)"       
## [142] "HOXC6_(+)"        "HOXC8_(+)"        "HOXD1_(+)"       
## [145] "HOXD10_(+)"       "HOXD4_(+)"        "HOXD8_(+)"       
## [148] "HOXD9_(+)"        "HSF1_(+)"         "HSF2_(+)"        
## [151] "IKZF2_(+)"        "ING3_(+)"         "IRF1_(+)"        
## [154] "IRF2_(+)"         "IRF4_(+)"         "IRF5_(+)"        
## [157] "IRF6_(+)"         "IRF7_(+)"         "IRF8_(+)"        
## [160] "IRF9_(+)"         "IRX2_(+)"         "ISL2_(+)"        
## [163] "JUN_(+)"          "JUND_(+)"         "KDM4D_(+)"       
## [166] "KDM5A_(+)"        "KLF10_(+)"        "KLF11_(+)"       
## [169] "KLF12_(+)"        "KLF13_(+)"        "KLF14_(+)"       
## [172] "KLF15_(+)"        "KLF16_(+)"        "KLF2_(+)"        
## [175] "KLF5_(+)"         "KLF6_(+)"         "KLF7_(+)"        
## [178] "KLF8_(+)"         "KLF9_(+)"         "LBX1_(+)"        
## [181] "LHX1_(+)"         "LHX4_(+)"         "LHX5_(+)"        
## [184] "LMX1B_(+)"        "MAFA_(+)"         "MAFB_(+)"        
## [187] "MAFK_(+)"         "MAX_(+)"          "MAZ_(+)"         
## [190] "MECOM_(+)"        "MEF2C_(+)"        "MEIS1_(+)"       
## [193] "MEOX2_(+)"        "MESP1_(+)"        "MIOS_(+)"        
## [196] "MITF_(+)"         "MLXIP_(+)"        "MLXIPL_(+)"      
## [199] "MXI1_(+)"         "MYBL1_(+)"        "MYCN_(+)"        
## [202] "MYEF2_(+)"        "MYOD1_(+)"        "MYPOP_(+)"       
## [205] "MZF1_(+)"         "NEUROD1_(+)"      "NFATC2_(+)"      
## [208] "NFE2_(+)"         "NFE2L1_(+)"       "NFE2L2_(+)"      
## [211] "NFE2L3_(+)"       "NFIC_(+)"         "NFKB1_(+)"       
## [214] "NFYA_(+)"         "NFYC_(+)"         "NHLH1_(+)"       
## [217] "NHLH2_(+)"        "NKX3-1_(+)"       "NKX6-2_(+)"      
## [220] "NPAS2_(+)"        "NPDC1_(+)"        "NR0B1_(+)"       
## [223] "NR1H2_(+)"        "NR1H3_(+)"        "NR1H4_(+)"       
## [226] "NR1I2_(+)"        "NR2E1_(+)"        "NR2F1_(+)"       
## [229] "NR2F6_(+)"        "NR4A1_(+)"        "NR5A2_(+)"       
## [232] "NRF1_(+)"         "OLIG2_(+)"        "OLIG3_(+)"       
## [235] "ONECUT2_(+)"      "OTP_(+)"          "OVOL1_(+)"       
## [238] "PAX7_(+)"         "PAX8_(+)"         "PAX9_(+)"        
## [241] "PBX1_(+)"         "PDX1_(+)"         "PHF2_(+)"        
## [244] "PHF21A_(+)"       "PHF8_(+)"         "PHOX2A_(+)"      
## [247] "PKNOX1_(+)"       "POLE3_(+)"        "POLR2A_(+)"      
## [250] "POLR3A_(+)"       "POU2F1_(+)"       "POU4F1_(+)"      
## [253] "POU5F1_(+)"       "POU5F1B_(+)"      "POU6F1_(+)"      
## [256] "PPARA_(+)"        "PPARD_(+)"        "PRDM1_(+)"       
## [259] "PRDM16_(+)"       "PRRX1_(+)"        "PRRX2_(+)"       
## [262] "RAD21_(+)"        "RARA_(+)"         "RARG_(+)"        
## [265] "RBBP5_(+)"        "REL_(+)"          "RFX7_(+)"        
## [268] "RREB1_(+)"        "RUNX2_(+)"        "SATB1_(+)"       
## [271] "SETDB1_(+)"       "SHOX2_(+)"        "SIN3A_(+)"       
## [274] "SIX1_(+)"         "SIX2_(+)"         "SIX5_(+)"        
## [277] "SMAD1_(+)"        "SMARCA5_(+)"      "SMARCC2_(+)"     
## [280] "SMC3_(+)"         "SNAI3_(+)"        "SNAPC4_(+)"      
## [283] "SOX11_(+)"        "SOX13_(+)"        "SOX15_(+)"       
## [286] "SOX2_(+)"         "SOX21_(+)"        "SOX4_(+)"        
## [289] "SOX9_(+)"         "SP1_(+)"          "SP2_(+)"         
## [292] "SP6_(+)"          "SP7_(+)"          "SP9_(+)"         
## [295] "SPDEF_(+)"        "SREBF2_(+)"       "SRF_(+)"         
## [298] "STAT1_(+)"        "STAT2_(+)"        "STAT4_(+)"       
## [301] "STAT5B_(+)"       "STAU2_(+)"        "TAF7_(+)"        
## [304] "TAL1_(+)"         "TBP_(+)"          "TBPL2_(+)"       
## [307] "TBX15_(+)"        "TBX18_(+)"        "TBX20_(+)"       
## [310] "TBX6_(+)"         "TCF3_(+)"         "TCF4_(+)"        
## [313] "TCF7_(+)"         "TCF7L1_(+)"       "TEAD4_(+)"       
## [316] "TET1_(+)"         "TFAP2A_(+)"       "TFAP2C_(+)"      
## [319] "TFDP1_(+)"        "TFDP2_(+)"        "TFE3_(+)"        
## [322] "TFEB_(+)"         "TGIF2_(+)"        "THAP1_(+)"       
## [325] "TLX1_(+)"         "TLX2_(+)"         "TP73_(+)"        
## [328] "TRIM28_(+)"       "UBP1_(+)"         "USF1_(+)"        
## [331] "VAX1_(+)"         "VAX2_(+)"         "VDR_(+)"         
## [334] "VEZF1_(+)"        "VSX1_(+)"         "VSX2_(+)"        
## [337] "WT1_(+)"          "YBX1_(+)"         "YY2_(+)"         
## [340] "ZBTB33_(+)"       "ZEB1_(+)"         "ZFHX2_(+)"       
## [343] "ZFY_(+)"          "ZNF134_(+)"       "ZNF143_(+)"      
## [346] "ZNF160_(+)"       "ZNF208_(+)"       "ZNF219_(+)"      
## [349] "ZNF25_(+)"        "ZNF264_(+)"       "ZNF267_(+)"      
## [352] "ZNF276_(+)"       "ZNF316_(+)"       "ZNF354C_(+)"     
## [355] "ZNF384_(+)"       "ZNF429_(+)"       "ZNF441_(+)"      
## [358] "ZNF471_(+)"       "ZNF483_(+)"       "ZNF486_(+)"      
## [361] "ZNF513_(+)"       "ZNF524_(+)"       "ZNF550_(+)"      
## [364] "ZNF554_(+)"       "ZNF560_(+)"       "ZNF606_(+)"      
## [367] "ZNF607_(+)"       "ZNF668_(+)"       "ZNF672_(+)"      
## [370] "ZNF713_(+)"       "ZNF717_(+)"       "ZNF721_(+)"      
## [373] "ZNF761_(+)"       "ZNF768_(+)"       "ZNF787_(+)"      
## [376] "ZNF8_(+)"         "ZSCAN31_(+)"      "ZXDC_(+)"        
## 
## $SARSCoV2_infected_NHBE
##   [1] "AHCTF1_(+)"  "AIRE_(+)"    "ALX1_(+)"    "ARID5B_(+)"  "ARNT_(+)"   
##   [6] "ATF1_(+)"    "BATF_(+)"    "BBX_(+)"     "BCL3_(+)"    "BCL6B_(+)"  
##  [11] "CEBPB_(+)"   "CEBPG_(+)"   "CKMT1B_(+)"  "CREB1_(+)"   "CREB3_(+)"  
##  [16] "CREBL2_(+)"  "DLX4_(+)"    "DMRT1_(+)"   "DMRTA1_(+)"  "DUXA_(+)"   
##  [21] "EBF1_(+)"    "EGR2_(+)"    "ERF_(+)"     "ESRRA_(+)"   "ETV1_(+)"   
##  [26] "ETV6_(+)"    "ETV7_(+)"    "FOSL1_(+)"   "FOXA2_(+)"   "FOXF2_(+)"  
##  [31] "FOXK2_(+)"   "FOXP3_(+)"   "FOXQ1_(+)"   "GATA2_(+)"   "GATA3_(+)"  
##  [36] "HDAC2_(+)"   "HES5_(+)"    "HLF_(+)"     "HNF1A_(+)"   "HNF1B_(+)"  
##  [41] "HOXA2_(+)"   "HOXA5_(+)"   "HOXA7_(+)"   "HOXA9_(+)"   "HOXB5_(+)"  
##  [46] "HOXB6_(+)"   "HOXB7_(+)"   "HOXB8_(+)"   "HOXB9_(+)"   "HOXC10_(+)" 
##  [51] "HOXC4_(+)"   "HOXC5_(+)"   "HOXC6_(+)"   "HOXC8_(+)"   "HSF2_(+)"   
##  [56] "ING3_(+)"    "IRF1_(+)"    "IRF3_(+)"    "IRF4_(+)"    "IRF5_(+)"   
##  [61] "IRF8_(+)"    "IRF9_(+)"    "IRX2_(+)"    "ISL2_(+)"    "JUN_(+)"    
##  [66] "KLF10_(+)"   "KLF5_(+)"    "LHX1_(+)"    "LHX4_(+)"    "LHX8_(+)"   
##  [71] "LHX9_(+)"    "MAFF_(+)"    "MEOX2_(+)"   "MIOS_(+)"    "MLXIP_(+)"  
##  [76] "MSX1_(+)"    "MSX2_(+)"    "MXD4_(+)"    "MYEF2_(+)"   "NFIL3_(+)"  
##  [81] "NFYB_(+)"    "NHLH1_(+)"   "NKX2-1_(+)"  "NKX3-1_(+)"  "NR1I2_(+)"  
##  [86] "NR4A1_(+)"   "NRF1_(+)"    "ONECUT2_(+)" "OVOL2_(+)"   "PAX2_(+)"   
##  [91] "PAX7_(+)"    "PBX1_(+)"    "PDX1_(+)"    "PKNOX1_(+)"  "POU2F3_(+)" 
##  [96] "PRDM16_(+)"  "RARG_(+)"    "RBBP5_(+)"   "RELA_(+)"    "RFX5_(+)"   
## [101] "SIX2_(+)"    "SMC3_(+)"    "SOX13_(+)"   "SOX2_(+)"    "SP1_(+)"    
## [106] "SP2_(+)"     "SP4_(+)"     "SP7_(+)"     "SREBF2_(+)"  "STAT1_(+)"  
## [111] "STAT2_(+)"   "TAF7_(+)"    "TAGLN2_(+)"  "TAL1_(+)"    "TBP_(+)"    
## [116] "TBPL1_(+)"   "TBPL2_(+)"   "TBX15_(+)"   "TBX3_(+)"    "TCF7_(+)"   
## [121] "TET1_(+)"    "TFAP2A_(+)"  "TFE3_(+)"    "TFEB_(+)"    "TLX3_(+)"   
## [126] "TWIST1_(+)"  "UBTF_(+)"    "UQCRB_(+)"   "VSX1_(+)"    "WT1_(+)"    
## [131] "ZEB1_(+)"    "ZFHX2_(+)"   "ZFY_(+)"     "ZNF160_(+)"  "ZNF471_(+)" 
## [136] "ZNF502_(+)"  "ZNF560_(+)"  "ZNF580_(+)"  "ZNF768_(+)"  "ZNF773_(+)" 
## [141] "ZXDC_(+)"   
## 
## $human_IFNB_treated_NHBE
##  [1] "ATF3_(+)"    "BACH2_(+)"   "ELF3_(+)"    "ETV6_(+)"    "ETV7_(+)"   
##  [6] "FOXA1_(+)"   "FOXK1_(+)"   "GATA2_(+)"   "GCM1_(+)"    "GTF2B_(+)"  
## [11] "HIVEP2_(+)"  "HLX_(+)"     "HOXD11_(+)"  "IRF1_(+)"    "IRF2_(+)"   
## [16] "IRF7_(+)"    "IRF8_(+)"    "IRF9_(+)"    "NFIL3_(+)"   "NFIX_(+)"   
## [21] "NKX3-1_(+)"  "POU5F1B_(+)" "PRDM16_(+)"  "RARA_(+)"    "RELA_(+)"   
## [26] "RXRB_(+)"    "SOX11_(+)"   "SOX9_(+)"    "STAT2_(+)"   "TFEB_(+)"   
## [31] "VEZF1_(+)"
tfs_da_down
## $HPIV3_infected_A549
##   [1] "ALX3_(+)"    "ALX4_(+)"    "ARNT_(+)"    "ARNTL_(+)"   "ATF1_(+)"   
##   [6] "ATF4_(+)"    "ATF5_(+)"    "BCL6B_(+)"   "BHLHE40_(+)" "BHLHE41_(+)"
##  [11] "BRF1_(+)"    "CDX1_(+)"    "CHD2_(+)"    "CLOCK_(+)"   "CPEB1_(+)"  
##  [16] "CREB1_(+)"   "CREB5_(+)"   "DDIT3_(+)"   "DLX2_(+)"    "E2F1_(+)"   
##  [21] "E4F1_(+)"    "ELF2_(+)"    "ESRRA_(+)"   "FOSL1_(+)"   "FOXA2_(+)"  
##  [26] "FOXB1_(+)"   "FOXC2_(+)"   "FOXF2_(+)"   "FOXK1_(+)"   "FOXO1_(+)"  
##  [31] "FOXO3_(+)"   "FOXP2_(+)"   "GABPB1_(+)"  "GCM1_(+)"    "HAND1_(+)"  
##  [36] "HES6_(+)"    "HEY1_(+)"    "HEY2_(+)"    "HIVEP2_(+)"  "HLF_(+)"    
##  [41] "HOXA9_(+)"   "HOXB2_(+)"   "HOXB6_(+)"   "HOXB8_(+)"   "HOXB9_(+)"  
##  [46] "HOXC10_(+)"  "HOXC13_(+)"  "HOXC8_(+)"   "HOXD11_(+)"  "HSF2_(+)"   
##  [51] "IKZF2_(+)"   "IRF4_(+)"    "ISL2_(+)"    "KDM5A_(+)"   "KLF3_(+)"   
##  [56] "KLF7_(+)"    "KLF9_(+)"    "LHX4_(+)"    "MAF_(+)"     "MAZ_(+)"    
##  [61] "MECOM_(+)"   "MXD3_(+)"    "MXI1_(+)"    "MYCN_(+)"    "MYEF2_(+)"  
##  [66] "NEUROD1_(+)" "NFE2L1_(+)"  "NFIA_(+)"    "NFIL3_(+)"   "NFKB1_(+)"  
##  [71] "NFKB2_(+)"   "NFYA_(+)"    "NFYC_(+)"    "NHLH1_(+)"   "NKX3-1_(+)" 
##  [76] "NR2C1_(+)"   "NR5A2_(+)"   "OTP_(+)"     "PAX7_(+)"    "POU3F2_(+)" 
##  [81] "POU5F1_(+)"  "RARB_(+)"    "RFX2_(+)"    "RFX3_(+)"    "RREB1_(+)"  
##  [86] "RUNX2_(+)"   "SNAI3_(+)"   "SOX1_(+)"    "SOX15_(+)"   "SP6_(+)"    
##  [91] "TAF7_(+)"    "TAGLN2_(+)"  "TAL1_(+)"    "TBX15_(+)"   "TBX20_(+)"  
##  [96] "TCF3_(+)"    "TFE3_(+)"    "TFEB_(+)"    "THAP1_(+)"   "VSX1_(+)"   
## [101] "ZBTB33_(+)"  "ZBTB7A_(+)"  "ZEB1_(+)"    "ZFX_(+)"     "ZIC2_(+)"   
## [106] "ZNF134_(+)"  "ZNF143_(+)"  "ZNF148_(+)"  "ZNF160_(+)"  "ZNF227_(+)" 
## [111] "ZNF354C_(+)" "ZNF429_(+)"  "ZNF449_(+)"  "ZNF502_(+)"  "ZNF524_(+)" 
## [116] "ZNF571_(+)"  "ZNF597_(+)"  "ZNF607_(+)"  "ZNF668_(+)"  "ZNF672_(+)" 
## [121] "ZNF787_(+)"  "ZNF841_(+)"  "ZSCAN26_(+)"
## 
## $IAV_infected_A549
##   [1] "ALX1_(+)"     "ALX4_(+)"     "ARNT_(+)"     "ARNT2_(+)"    "ARNTL2_(+)"  
##   [6] "ASCL2_(+)"    "ATF2_(+)"     "ATF4_(+)"     "BACH1_(+)"    "BATF_(+)"    
##  [11] "BBX_(+)"      "BCL11A_(+)"   "BCL11B_(+)"   "BCLAF1_(+)"   "BHLHE40_(+)" 
##  [16] "BRF1_(+)"     "CDX2_(+)"     "CLOCK_(+)"    "CPEB1_(+)"    "CREB5_(+)"   
##  [21] "CTCFL_(+)"    "DLX3_(+)"     "DLX5_(+)"     "E2F1_(+)"     "E2F2_(+)"    
##  [26] "E2F4_(+)"     "E2F5_(+)"     "E2F6_(+)"     "E2F8_(+)"     "EGR1_(+)"    
##  [31] "EGR3_(+)"     "EHF_(+)"      "ELF1_(+)"     "ELF4_(+)"     "ELF5_(+)"    
##  [36] "ELK3_(+)"     "ELK4_(+)"     "EN1_(+)"      "EN2_(+)"      "ERF_(+)"     
##  [41] "ESRRA_(+)"    "ETS1_(+)"     "ETS2_(+)"     "ETV1_(+)"     "ETV7_(+)"    
##  [46] "FOSB_(+)"     "FOSL2_(+)"    "FOXB1_(+)"    "FOXC1_(+)"    "FOXD3_(+)"   
##  [51] "FOXF2_(+)"    "FOXM1_(+)"    "FOXO1_(+)"    "GABPA_(+)"    "GABPB1_(+)"  
##  [56] "GATA5_(+)"    "GCM1_(+)"     "GLI1_(+)"     "GLIS2_(+)"    "GRHL1_(+)"   
##  [61] "GRHL3_(+)"    "GRHPR_(+)"    "GSC_(+)"      "GSX2_(+)"     "GTF2B_(+)"   
##  [66] "GTF2IRD1_(+)" "HES1_(+)"     "HES5_(+)"     "HES6_(+)"     "HIC1_(+)"    
##  [71] "HINFP_(+)"    "HIVEP2_(+)"   "HLX_(+)"      "HNF1A_(+)"    "HNF1B_(+)"   
##  [76] "HOXA1_(+)"    "HOXA2_(+)"    "HOXA5_(+)"    "HOXA6_(+)"    "HOXA7_(+)"   
##  [81] "HOXA9_(+)"    "HOXB13_(+)"   "HOXB5_(+)"    "HOXB7_(+)"    "HOXB8_(+)"   
##  [86] "HOXC10_(+)"   "HOXC11_(+)"   "HOXC13_(+)"   "HOXC5_(+)"    "HOXC6_(+)"   
##  [91] "HOXD3_(+)"    "HOXD4_(+)"    "HOXD9_(+)"    "HTATIP2_(+)"  "IRF1_(+)"    
##  [96] "IRF2_(+)"     "IRF3_(+)"     "IRF5_(+)"     "IRF6_(+)"     "IRF7_(+)"    
## [101] "IRF9_(+)"     "IRX1_(+)"     "IRX2_(+)"     "IRX4_(+)"     "IRX5_(+)"    
## [106] "JUND_(+)"     "KLF10_(+)"    "KLF3_(+)"     "KLF4_(+)"     "KLF5_(+)"    
## [111] "KLF6_(+)"     "KLF8_(+)"     "KLF9_(+)"     "LBX2_(+)"     "LHX2_(+)"    
## [116] "LHX5_(+)"     "LMX1B_(+)"    "MAFA_(+)"     "MAFB_(+)"     "MAFG_(+)"    
## [121] "MAX_(+)"      "MAZ_(+)"      "MECOM_(+)"    "MEOX1_(+)"    "MNX1_(+)"    
## [126] "MSX2_(+)"     "MTF1_(+)"     "MXD1_(+)"     "MXD3_(+)"     "MXD4_(+)"    
## [131] "MXI1_(+)"     "MYCN_(+)"     "MYEF2_(+)"    "MYPOP_(+)"    "MZF1_(+)"    
## [136] "NEUROD1_(+)"  "NFATC4_(+)"   "NFE2_(+)"     "NFE2L1_(+)"   "NFIA_(+)"    
## [141] "NFKB1_(+)"    "NFYA_(+)"     "NFYC_(+)"     "NHLH2_(+)"    "NKX2-1_(+)"  
## [146] "NKX3-1_(+)"   "NR1H3_(+)"    "NR1H4_(+)"    "NR2E1_(+)"    "NR2F1_(+)"   
## [151] "NR2F6_(+)"    "ONECUT2_(+)"  "OTP_(+)"      "OTX1_(+)"     "OVOL2_(+)"   
## [156] "PAX7_(+)"     "PAX9_(+)"     "PHF21A_(+)"   "PHF8_(+)"     "PKNOX1_(+)"  
## [161] "POLE4_(+)"    "POLR2A_(+)"   "POLR3A_(+)"   "POLR3G_(+)"   "POU2F1_(+)"  
## [166] "POU2F3_(+)"   "POU3F1_(+)"   "POU3F4_(+)"   "PPARD_(+)"    "PRDM1_(+)"   
## [171] "PRDM15_(+)"   "PRRX2_(+)"    "PSMD12_(+)"   "RAB18_(+)"    "RARG_(+)"    
## [176] "REL_(+)"      "RFX2_(+)"     "RORA_(+)"     "RREB1_(+)"    "RXRG_(+)"    
## [181] "SATB1_(+)"    "SETDB1_(+)"   "SIN3A_(+)"    "SIX2_(+)"     "SIX5_(+)"    
## [186] "SMAD1_(+)"    "SMARCA5_(+)"  "SMARCC2_(+)"  "SNAI2_(+)"    "SNAI3_(+)"   
## [191] "SOX5_(+)"     "SP3_(+)"      "SP5_(+)"      "STAT1_(+)"    "STAT2_(+)"   
## [196] "STAT5A_(+)"   "STAT5B_(+)"   "TAGLN2_(+)"   "TBPL2_(+)"    "TCF12_(+)"   
## [201] "TCF3_(+)"     "TCF7_(+)"     "TEAD4_(+)"    "TEF_(+)"      "TFAP2A_(+)"  
## [206] "TFAP2C_(+)"   "TFAP2E_(+)"   "TFDP2_(+)"    "TGIF2_(+)"    "TLX2_(+)"    
## [211] "TRIM28_(+)"   "USF1_(+)"     "USF2_(+)"     "VAX1_(+)"     "VDR_(+)"     
## [216] "VSX2_(+)"     "ZBTB7A_(+)"   "ZFX_(+)"      "ZNF134_(+)"   "ZNF143_(+)"  
## [221] "ZNF208_(+)"   "ZNF219_(+)"   "ZNF274_(+)"   "ZNF281_(+)"   "ZNF35_(+)"   
## [226] "ZNF354C_(+)"  "ZNF426_(+)"   "ZNF429_(+)"   "ZNF471_(+)"   "ZNF483_(+)"  
## [231] "ZNF502_(+)"   "ZNF524_(+)"   "ZNF554_(+)"   "ZNF560_(+)"   "ZNF597_(+)"  
## [236] "ZNF672_(+)"   "ZNF682_(+)"   "ZNF720_(+)"   "ZNF729_(+)"   "ZNF730_(+)"  
## [241] "ZNF761_(+)"   "ZNF773_(+)"   "ZNF787_(+)"  
## 
## $IAV_infected_NHBE
##   [1] "AHCTF1_(+)"       "AIRE_(+)"         "ALX1_(+)"        
##   [4] "ALX3_(+)"         "ALX4_(+)"         "AR_(+)"          
##   [7] "ARID5B_(+)"       "ARNT_(+)"         "ARNTL2_(+)"      
##  [10] "ATF1_(+)"         "ATF3_(+)"         "BACH2_(+)"       
##  [13] "BATF_(+)"         "BCL3_(+)"         "BCLAF1_(+)"      
##  [16] "BDP1_(+)"         "BHLHE41_(+)"      "BNC2_(+)"        
##  [19] "BORCS8-MEF2B_(+)" "BRF1_(+)"         "CCNT2_(+)"       
##  [22] "CDX2_(+)"         "CEBPA_(+)"        "CEBPB_(+)"       
##  [25] "CEBPD_(+)"        "CELF6_(+)"        "CHD2_(+)"        
##  [28] "CKMT1B_(+)"       "CLOCK_(+)"        "CNOT3_(+)"       
##  [31] "CPEB1_(+)"        "CPSF4_(+)"        "CREB1_(+)"       
##  [34] "CREB3_(+)"        "CREB3L1_(+)"      "CUX1_(+)"        
##  [37] "DBX1_(+)"         "DLX2_(+)"         "DLX4_(+)"        
##  [40] "DMRT1_(+)"        "DMRTA1_(+)"       "DUXA_(+)"        
##  [43] "E2F3_(+)"         "E2F4_(+)"         "E2F6_(+)"        
##  [46] "EGR1_(+)"         "EGR2_(+)"         "EGR3_(+)"        
##  [49] "ELK3_(+)"         "EMX1_(+)"         "EN1_(+)"         
##  [52] "EN2_(+)"          "ENO1_(+)"         "EP300_(+)"       
##  [55] "ERF_(+)"          "ESRRA_(+)"        "ESRRB_(+)"       
##  [58] "ETV1_(+)"         "ETV3_(+)"         "ETV5_(+)"        
##  [61] "EVX2_(+)"         "FGF19_(+)"        "FOS_(+)"         
##  [64] "FOSL1_(+)"        "FOXA1_(+)"        "FOXA2_(+)"       
##  [67] "FOXB1_(+)"        "FOXC1_(+)"        "FOXC2_(+)"       
##  [70] "FOXD2_(+)"        "FOXD3_(+)"        "FOXD4_(+)"       
##  [73] "FOXD4L6_(+)"      "FOXF2_(+)"        "FOXJ2_(+)"       
##  [76] "FOXK1_(+)"        "FOXK2_(+)"        "FOXM1_(+)"       
##  [79] "FOXN1_(+)"        "FOXO1_(+)"        "FOXO3_(+)"       
##  [82] "FOXO6_(+)"        "FOXQ1_(+)"        "GATA3_(+)"       
##  [85] "GCM1_(+)"         "GLIS2_(+)"        "GMEB1_(+)"       
##  [88] "GRHL2_(+)"        "GTF2IRD1_(+)"     "HAND1_(+)"       
##  [91] "HDAC1_(+)"        "HES5_(+)"         "HEY1_(+)"        
##  [94] "HINFP_(+)"        "HLF_(+)"          "HMGB1_(+)"       
##  [97] "HNF1A_(+)"        "HNF1B_(+)"        "HOXA10_(+)"      
## [100] "HOXA2_(+)"        "HOXA5_(+)"        "HOXA9_(+)"       
## [103] "HOXB13_(+)"       "HOXB4_(+)"        "HOXB6_(+)"       
## [106] "HOXB8_(+)"        "HOXB9_(+)"        "HOXC10_(+)"      
## [109] "HOXC13_(+)"       "HOXC4_(+)"        "HOXC6_(+)"       
## [112] "HOXC8_(+)"        "HOXC9_(+)"        "HOXD11_(+)"      
## [115] "HOXD13_(+)"       "HOXD3_(+)"        "HOXD4_(+)"       
## [118] "HSF2_(+)"         "HSF4_(+)"         "HTATIP2_(+)"     
## [121] "IKZF3_(+)"        "ING3_(+)"         "IRF1_(+)"        
## [124] "IRF4_(+)"         "IRX2_(+)"         "IRX5_(+)"        
## [127] "ISL2_(+)"         "JUN_(+)"          "JUNB_(+)"        
## [130] "JUND_(+)"         "KDM5A_(+)"        "KLF1_(+)"        
## [133] "KLF10_(+)"        "KLF11_(+)"        "KLF12_(+)"       
## [136] "KLF13_(+)"        "KLF14_(+)"        "KLF2_(+)"        
## [139] "KLF5_(+)"         "KLF8_(+)"         "LHX4_(+)"        
## [142] "LHX8_(+)"         "LHX9_(+)"         "LMX1B_(+)"       
## [145] "MAF_(+)"          "MAFB_(+)"         "MAFF_(+)"        
## [148] "MAFG_(+)"         "MEF2B_(+)"        "MEF2C_(+)"       
## [151] "MEOX2_(+)"        "MLXIP_(+)"        "MLXIPL_(+)"      
## [154] "MNT_(+)"          "MNX1_(+)"         "MSX1_(+)"        
## [157] "MSX2_(+)"         "MYEF2_(+)"        "MYOD1_(+)"       
## [160] "MZF1_(+)"         "NFATC2_(+)"       "NFE2L2_(+)"      
## [163] "NFE2L3_(+)"       "NFIA_(+)"         "NFIB_(+)"        
## [166] "NFIC_(+)"         "NFIL3_(+)"        "NFKB2_(+)"       
## [169] "NHLH1_(+)"        "NKX2-1_(+)"       "NKX2-5_(+)"      
## [172] "NKX3-1_(+)"       "NPDC1_(+)"        "NR0B1_(+)"       
## [175] "NR1D1_(+)"        "NR2E1_(+)"        "NR2F1_(+)"       
## [178] "NR3C1_(+)"        "NR4A1_(+)"        "NR5A2_(+)"       
## [181] "NR6A1_(+)"        "NRF1_(+)"         "ONECUT1_(+)"     
## [184] "ONECUT2_(+)"      "ONECUT3_(+)"      "OTP_(+)"         
## [187] "PATZ1_(+)"        "PAX7_(+)"         "PDX1_(+)"        
## [190] "PKNOX1_(+)"       "POLE3_(+)"        "POLR2A_(+)"      
## [193] "POLR3G_(+)"       "POU3F2_(+)"       "POU3F4_(+)"      
## [196] "POU5F1_(+)"       "PPARD_(+)"        "PROX1_(+)"       
## [199] "PRRX1_(+)"        "PSMD12_(+)"       "RARB_(+)"        
## [202] "RARG_(+)"         "RBBP5_(+)"        "REL_(+)"         
## [205] "RELA_(+)"         "RFX1_(+)"         "RFX2_(+)"        
## [208] "RFX3_(+)"         "RFX5_(+)"         "RFXAP_(+)"       
## [211] "SATB1_(+)"        "SIN3A_(+)"        "SIX2_(+)"        
## [214] "SIX4_(+)"         "SIX5_(+)"         "SOHLH2_(+)"      
## [217] "SOX1_(+)"         "SOX13_(+)"        "SOX15_(+)"       
## [220] "SOX2_(+)"         "SOX21_(+)"        "SOX4_(+)"        
## [223] "SOX6_(+)"         "SP7_(+)"          "SP9_(+)"         
## [226] "SPDEF_(+)"        "SREBF2_(+)"       "STAT4_(+)"       
## [229] "TAF7_(+)"         "TAGLN2_(+)"       "TAL1_(+)"        
## [232] "TBP_(+)"          "TBPL1_(+)"        "TBX15_(+)"       
## [235] "TBX20_(+)"        "TBX3_(+)"         "TBX6_(+)"        
## [238] "TCF4_(+)"         "TCF7_(+)"         "TET1_(+)"        
## [241] "TFAP2A_(+)"       "TFDP1_(+)"        "TFE3_(+)"        
## [244] "TFEB_(+)"         "THAP1_(+)"        "TLX2_(+)"        
## [247] "TLX3_(+)"         "TRPS1_(+)"        "UQCRB_(+)"       
## [250] "USF2_(+)"         "VEZF1_(+)"        "VSX1_(+)"        
## [253] "VSX2_(+)"         "XBP1_(+)"         "YBX1_(+)"        
## [256] "ZBTB41_(+)"       "ZBTB43_(+)"       "ZEB1_(+)"        
## [259] "ZFHX2_(+)"        "ZIC2_(+)"         "ZNF160_(+)"      
## [262] "ZNF189_(+)"       "ZNF208_(+)"       "ZNF239_(+)"      
## [265] "ZNF263_(+)"       "ZNF264_(+)"       "ZNF274_(+)"      
## [268] "ZNF281_(+)"       "ZNF316_(+)"       "ZNF441_(+)"      
## [271] "ZNF442_(+)"       "ZNF467_(+)"       "ZNF471_(+)"      
## [274] "ZNF486_(+)"       "ZNF502_(+)"       "ZNF513_(+)"      
## [277] "ZNF560_(+)"       "ZNF571_(+)"       "ZNF597_(+)"      
## [280] "ZNF668_(+)"       "ZNF713_(+)"       "ZNF721_(+)"      
## [283] "ZNF740_(+)"       "ZNF816_(+)"       "ZNF836_(+)"      
## [286] "ZSCAN31_(+)"      "ZXDC_(+)"        
## 
## $IAVdNS1_infected_NHBE
##   [1] "AIRE_(+)"     "ALX1_(+)"     "AR_(+)"       "ARNT_(+)"     "ARNTL2_(+)"  
##   [6] "ATF1_(+)"     "ATF3_(+)"     "ATF5_(+)"     "BACH2_(+)"    "BATF_(+)"    
##  [11] "BCL3_(+)"     "BCLAF1_(+)"   "BDP1_(+)"     "BHLHE40_(+)"  "BHLHE41_(+)" 
##  [16] "BNC2_(+)"     "BRF1_(+)"     "CCNT2_(+)"    "CDX2_(+)"     "CEBPA_(+)"   
##  [21] "CEBPB_(+)"    "CEBPD_(+)"    "CELF6_(+)"    "CHD2_(+)"     "CKMT1B_(+)"  
##  [26] "CNOT3_(+)"    "CPSF4_(+)"    "CREB1_(+)"    "CREB3_(+)"    "CREB3L1_(+)" 
##  [31] "CTCF_(+)"     "DBX1_(+)"     "DDIT3_(+)"    "DLX2_(+)"     "E2F3_(+)"    
##  [36] "E2F4_(+)"     "E2F6_(+)"     "E2F8_(+)"     "EGR1_(+)"     "EGR2_(+)"    
##  [41] "EGR3_(+)"     "ELK3_(+)"     "EMX1_(+)"     "EN2_(+)"      "ENO1_(+)"    
##  [46] "EP300_(+)"    "ERF_(+)"      "ESR2_(+)"     "ESRRA_(+)"    "ESRRB_(+)"   
##  [51] "ETV1_(+)"     "ETV3_(+)"     "ETV5_(+)"     "EVX2_(+)"     "FGF19_(+)"   
##  [56] "FOS_(+)"      "FOSL1_(+)"    "FOXA1_(+)"    "FOXA2_(+)"    "FOXB1_(+)"   
##  [61] "FOXC1_(+)"    "FOXC2_(+)"    "FOXD2_(+)"    "FOXD3_(+)"    "FOXD4_(+)"   
##  [66] "FOXD4L4_(+)"  "FOXD4L6_(+)"  "FOXK1_(+)"    "FOXK2_(+)"    "FOXM1_(+)"   
##  [71] "FOXO1_(+)"    "FOXO3_(+)"    "FOXO6_(+)"    "FOXQ1_(+)"    "GATA3_(+)"   
##  [76] "GATA6_(+)"    "GCM1_(+)"     "GMEB1_(+)"    "GMEB2_(+)"    "GPD1_(+)"    
##  [81] "GRHL2_(+)"    "GSX1_(+)"     "GTF2IRD1_(+)" "HAND1_(+)"    "HDAC1_(+)"   
##  [86] "HES5_(+)"     "HIC1_(+)"     "HINFP_(+)"    "HLF_(+)"      "HMGB1_(+)"   
##  [91] "HNF1B_(+)"    "HOXA10_(+)"   "HOXA2_(+)"    "HOXA5_(+)"    "HOXA9_(+)"   
##  [96] "HOXB13_(+)"   "HOXB2_(+)"    "HOXB6_(+)"    "HOXB8_(+)"    "HOXB9_(+)"   
## [101] "HOXC10_(+)"   "HOXC13_(+)"   "HOXC4_(+)"    "HOXC6_(+)"    "HOXC8_(+)"   
## [106] "HOXC9_(+)"    "HOXD11_(+)"   "HOXD13_(+)"   "HOXD3_(+)"    "HOXD4_(+)"   
## [111] "HSF2_(+)"     "HSF4_(+)"     "HTATIP2_(+)"  "IKZF3_(+)"    "ING3_(+)"    
## [116] "IRF1_(+)"     "IRF4_(+)"     "IRX2_(+)"     "IRX5_(+)"     "ISL2_(+)"    
## [121] "JUN_(+)"      "JUNB_(+)"     "JUND_(+)"     "KDM5A_(+)"    "KLF1_(+)"    
## [126] "KLF11_(+)"    "KLF12_(+)"    "KLF14_(+)"    "KLF2_(+)"     "KLF5_(+)"    
## [131] "KLF8_(+)"     "LHX4_(+)"     "LHX8_(+)"     "LHX9_(+)"     "MAF_(+)"     
## [136] "MAFB_(+)"     "MAFF_(+)"     "MAFG_(+)"     "MEF2B_(+)"    "MLXIP_(+)"   
## [141] "MLXIPL_(+)"   "MNT_(+)"      "MNX1_(+)"     "MSX1_(+)"     "MSX2_(+)"    
## [146] "MXD4_(+)"     "MXI1_(+)"     "MYEF2_(+)"    "MYOD1_(+)"    "MYPOP_(+)"   
## [151] "MZF1_(+)"     "NFATC2_(+)"   "NFE2L1_(+)"   "NFE2L2_(+)"   "NFIA_(+)"    
## [156] "NFIB_(+)"     "NFIC_(+)"     "NFIL3_(+)"    "NFKB2_(+)"    "NHLH1_(+)"   
## [161] "NHLH2_(+)"    "NKX2-1_(+)"   "NKX3-1_(+)"   "NPDC1_(+)"    "NR0B1_(+)"   
## [166] "NR1D1_(+)"    "NR2C1_(+)"    "NR2F1_(+)"    "NR4A1_(+)"    "NR5A2_(+)"   
## [171] "NR6A1_(+)"    "NRF1_(+)"     "ONECUT1_(+)"  "ONECUT2_(+)"  "ONECUT3_(+)" 
## [176] "OTP_(+)"      "PATZ1_(+)"    "PAX7_(+)"     "PHF21A_(+)"   "PKNOX1_(+)"  
## [181] "POLE3_(+)"    "POLR2A_(+)"   "POLR3A_(+)"   "POLR3G_(+)"   "POU1F1_(+)"  
## [186] "POU3F2_(+)"   "POU3F4_(+)"   "POU4F3_(+)"   "POU5F1_(+)"   "PPARD_(+)"   
## [191] "PROX1_(+)"    "PSMD12_(+)"   "RARB_(+)"     "RARG_(+)"     "RBBP5_(+)"   
## [196] "REL_(+)"      "RELA_(+)"     "RFX1_(+)"     "RFX2_(+)"     "RFX3_(+)"    
## [201] "RFX5_(+)"     "RFXAP_(+)"    "SHOX2_(+)"    "SIX4_(+)"     "SIX5_(+)"    
## [206] "SMAD3_(+)"    "SNAPC4_(+)"   "SOHLH2_(+)"   "SOX1_(+)"     "SOX13_(+)"   
## [211] "SOX15_(+)"    "SOX21_(+)"    "SOX4_(+)"     "SOX6_(+)"     "SP9_(+)"     
## [216] "SPDEF_(+)"    "SREBF2_(+)"   "STAT4_(+)"    "TAF7_(+)"     "TAGLN2_(+)"  
## [221] "TAL1_(+)"     "TBP_(+)"      "TBPL1_(+)"    "TBX18_(+)"    "TBX20_(+)"   
## [226] "TBX3_(+)"     "TCF4_(+)"     "TCF7_(+)"     "TEF_(+)"      "TET1_(+)"    
## [231] "TFAP2A_(+)"   "TFDP1_(+)"    "TFE3_(+)"     "TFEB_(+)"     "THAP1_(+)"   
## [236] "TLX3_(+)"     "TRPS1_(+)"    "UBP1_(+)"     "UBTF_(+)"     "UQCRB_(+)"   
## [241] "VEZF1_(+)"    "VSX1_(+)"     "VSX2_(+)"     "XBP1_(+)"     "YBX1_(+)"    
## [246] "YY2_(+)"      "ZBTB41_(+)"   "ZBTB43_(+)"   "ZDHHC15_(+)"  "ZEB1_(+)"    
## [251] "ZFHX2_(+)"    "ZFHX3_(+)"    "ZFP64_(+)"    "ZFX_(+)"      "ZIC2_(+)"    
## [256] "ZNF143_(+)"   "ZNF160_(+)"   "ZNF205_(+)"   "ZNF208_(+)"   "ZNF239_(+)"  
## [261] "ZNF25_(+)"    "ZNF263_(+)"   "ZNF264_(+)"   "ZNF274_(+)"   "ZNF281_(+)"  
## [266] "ZNF316_(+)"   "ZNF426_(+)"   "ZNF441_(+)"   "ZNF449_(+)"   "ZNF467_(+)"  
## [271] "ZNF471_(+)"   "ZNF483_(+)"   "ZNF486_(+)"   "ZNF502_(+)"   "ZNF513_(+)"  
## [276] "ZNF560_(+)"   "ZNF571_(+)"   "ZNF597_(+)"   "ZNF668_(+)"   "ZNF713_(+)"  
## [281] "ZNF717_(+)"   "ZNF721_(+)"   "ZNF740_(+)"   "ZNF816_(+)"   "ZNF841_(+)"  
## [286] "ZSCAN31_(+)"  "ZXDC_(+)"    
## 
## $RSV_infected_A549
##  [1] "ARNT_(+)"    "BCLAF1_(+)"  "BHLHE40_(+)" "CDX1_(+)"    "CLOCK_(+)"  
##  [6] "CREB5_(+)"   "ELF2_(+)"    "ELK3_(+)"    "EP300_(+)"   "ETV1_(+)"   
## [11] "ETV3_(+)"    "FOSL2_(+)"   "GMEB1_(+)"   "HEY1_(+)"    "HOXB6_(+)"  
## [16] "IRX2_(+)"    "KLF7_(+)"    "MAX_(+)"     "MNX1_(+)"    "MXD3_(+)"   
## [21] "MYCN_(+)"    "NFATC2_(+)"  "NFKB1_(+)"   "NFYA_(+)"    "NFYC_(+)"   
## [26] "NKX3-1_(+)"  "NR2F1_(+)"   "PKNOX1_(+)"  "POLR3A_(+)"  "POLR3G_(+)" 
## [31] "PPARD_(+)"   "PRDM16_(+)"  "REL_(+)"     "RREB1_(+)"   "SMAD1_(+)"  
## [36] "SNAI3_(+)"   "SP5_(+)"     "TCF7_(+)"    "ZFX_(+)"     "ZNF208_(+)" 
## [41] "ZNF264_(+)"  "ZNF267_(+)"  "ZNF426_(+)"  "ZNF429_(+)"  "ZNF502_(+)" 
## [46] "ZNF560_(+)"  "ZNF773_(+)" 
## 
## $SARSCoV2_infected_A549
##   [1] "ALX1_(+)"     "ALX3_(+)"     "ALX4_(+)"     "ARNT_(+)"     "ARNT2_(+)"   
##   [6] "ARNTL2_(+)"   "ATF2_(+)"     "ATF4_(+)"     "ATF6_(+)"     "BACH1_(+)"   
##  [11] "BBX_(+)"      "BCL11A_(+)"   "BCL11B_(+)"   "BCLAF1_(+)"   "BHLHA15_(+)" 
##  [16] "BHLHE40_(+)"  "BRF1_(+)"     "CDX2_(+)"     "CELF6_(+)"    "CLOCK_(+)"   
##  [21] "CPEB1_(+)"    "CTCFL_(+)"    "DLX3_(+)"     "DLX4_(+)"     "DLX5_(+)"    
##  [26] "DRGX_(+)"     "E2F1_(+)"     "E2F2_(+)"     "E2F4_(+)"     "E2F5_(+)"    
##  [31] "EHF_(+)"      "ELF1_(+)"     "ELK1_(+)"     "ELK3_(+)"     "ELK4_(+)"    
##  [36] "EN1_(+)"      "ERF_(+)"      "ETS1_(+)"     "ETS2_(+)"     "ETV1_(+)"    
##  [41] "ETV3_(+)"     "FEV_(+)"      "FLI1_(+)"     "FOSL2_(+)"    "FOXA3_(+)"   
##  [46] "FOXD2_(+)"    "FOXD3_(+)"    "FOXF2_(+)"    "FOXP4_(+)"    "FOXQ1_(+)"   
##  [51] "GABPA_(+)"    "GABPB1_(+)"   "GATA5_(+)"    "GCM1_(+)"     "GLI1_(+)"    
##  [56] "GLIS2_(+)"    "GRHL3_(+)"    "GRHPR_(+)"    "GSX2_(+)"     "GTF2B_(+)"   
##  [61] "GTF2IRD1_(+)" "GTF3A_(+)"    "HES5_(+)"     "HES6_(+)"     "HEY1_(+)"    
##  [66] "HIC1_(+)"     "HLX_(+)"      "HNF1A_(+)"    "HNF1B_(+)"    "HOXA1_(+)"   
##  [71] "HOXA6_(+)"    "HOXA7_(+)"    "HOXB13_(+)"   "HOXB2_(+)"    "HOXB5_(+)"   
##  [76] "HOXB6_(+)"    "HOXB8_(+)"    "HOXC10_(+)"   "HOXC11_(+)"   "HOXC6_(+)"   
##  [81] "HOXD3_(+)"    "HOXD4_(+)"    "HOXD9_(+)"    "HSF4_(+)"     "HTATIP2_(+)" 
##  [86] "IKZF2_(+)"    "ING3_(+)"     "IRF2_(+)"     "IRF6_(+)"     "IRF9_(+)"    
##  [91] "IRX1_(+)"     "IRX2_(+)"     "IRX4_(+)"     "JUND_(+)"     "KLF10_(+)"   
##  [96] "KLF6_(+)"     "KLF7_(+)"     "KLF8_(+)"     "LBX2_(+)"     "LHX2_(+)"    
## [101] "LMX1B_(+)"    "MAF_(+)"      "MAFA_(+)"     "MAX_(+)"      "MAZ_(+)"     
## [106] "MECOM_(+)"    "MEOX1_(+)"    "MESP1_(+)"    "MNX1_(+)"     "MXD1_(+)"    
## [111] "MXD3_(+)"     "MXI1_(+)"     "MYCN_(+)"     "MYOD1_(+)"    "MYPOP_(+)"   
## [116] "MZF1_(+)"     "NEUROD1_(+)"  "NFATC4_(+)"   "NFE2L1_(+)"   "NFIA_(+)"    
## [121] "NFIB_(+)"     "NFKB1_(+)"    "NFYA_(+)"     "NFYC_(+)"     "NHLH2_(+)"   
## [126] "NKX2-1_(+)"   "NKX2-5_(+)"   "NKX3-1_(+)"   "NR1H3_(+)"    "NR1H4_(+)"   
## [131] "NR2E1_(+)"    "NR2F1_(+)"    "NR2F6_(+)"    "NR6A1_(+)"    "ONECUT2_(+)" 
## [136] "OTP_(+)"      "OTX1_(+)"     "PATZ1_(+)"    "PAX7_(+)"     "PAX9_(+)"    
## [141] "PHF8_(+)"     "PKNOX1_(+)"   "POLE4_(+)"    "POLR2A_(+)"   "POLR3A_(+)"  
## [146] "POLR3G_(+)"   "POU3F4_(+)"   "PRDM1_(+)"    "PRDM15_(+)"   "PRRX2_(+)"   
## [151] "PSMD12_(+)"   "RAB18_(+)"    "RB1_(+)"      "RFX1_(+)"     "RFX2_(+)"    
## [156] "RREB1_(+)"    "RUNX2_(+)"    "RXRG_(+)"     "SATB1_(+)"    "SHOX2_(+)"   
## [161] "SIN3A_(+)"    "SIX5_(+)"     "SMAD1_(+)"    "SMARCA5_(+)"  "SMARCC2_(+)" 
## [166] "SNAI1_(+)"    "SNAI2_(+)"    "SNAI3_(+)"    "SOX5_(+)"     "SP3_(+)"     
## [171] "SP5_(+)"      "SPDEF_(+)"    "STAT1_(+)"    "STAT5B_(+)"   "TAL2_(+)"    
## [176] "TCF3_(+)"     "TCF7L1_(+)"   "TCF7L2_(+)"   "TEAD2_(+)"    "TFAP2A_(+)"  
## [181] "TFAP2C_(+)"   "TFDP2_(+)"    "THRA_(+)"     "TLX1_(+)"     "TLX2_(+)"    
## [186] "TRIM28_(+)"   "USF1_(+)"     "USF2_(+)"     "VAX1_(+)"     "VSX2_(+)"    
## [191] "ZFHX3_(+)"    "ZFP64_(+)"    "ZFX_(+)"      "ZIC2_(+)"     "ZNF134_(+)"  
## [196] "ZNF143_(+)"   "ZNF219_(+)"   "ZNF267_(+)"   "ZNF281_(+)"   "ZNF319_(+)"  
## [201] "ZNF35_(+)"    "ZNF354C_(+)"  "ZNF426_(+)"   "ZNF429_(+)"   "ZNF471_(+)"  
## [206] "ZNF483_(+)"   "ZNF486_(+)"   "ZNF502_(+)"   "ZNF513_(+)"   "ZNF524_(+)"  
## [211] "ZNF554_(+)"   "ZNF560_(+)"   "ZNF583_(+)"   "ZNF597_(+)"   "ZNF672_(+)"  
## [216] "ZNF720_(+)"   "ZNF729_(+)"   "ZNF730_(+)"   "ZNF75A_(+)"   "ZNF768_(+)"  
## [221] "ZNF773_(+)"   "ZNF787_(+)"  
## 
## $SARSCoV2_infected_A549_hACE2
##  [1] "ATF3_(+)"    "CEBPD_(+)"   "DLX2_(+)"    "EGR3_(+)"    "EMX1_(+)"   
##  [6] "ETV6_(+)"    "ETV7_(+)"    "FOXK1_(+)"   "HIVEP2_(+)"  "HOXB6_(+)"  
## [11] "IRF1_(+)"    "IRF5_(+)"    "IRF8_(+)"    "IRF9_(+)"    "KLF13_(+)"  
## [16] "MEF2B_(+)"   "NEUROD2_(+)" "NFE2L2_(+)"  "NKX3-1_(+)"  "RXRG_(+)"   
## [21] "SMARCA5_(+)" "SOX2_(+)"    "SOX21_(+)"   "STAT1_(+)"   "STAT2_(+)"  
## [26] "TP53_(+)"    "TP73_(+)"    "XBP1_(+)"    "ZNF768_(+)" 
## 
## $SARSCoV2_infected_A549_hACE2_pt
##   [1] "AIRE_(+)"    "AKR1A1_(+)"  "ALX4_(+)"    "ARID5B_(+)"  "ARNT_(+)"   
##   [6] "ATF3_(+)"    "BCLAF1_(+)"  "BHLHA15_(+)" "BHLHE40_(+)" "BRF2_(+)"   
##  [11] "CDX2_(+)"    "CEBPA_(+)"   "CEBPD_(+)"   "CLOCK_(+)"   "CTCFL_(+)"  
##  [16] "DLX2_(+)"    "DLX3_(+)"    "DLX4_(+)"    "DMRT1_(+)"   "DMRTA1_(+)" 
##  [21] "E2F1_(+)"    "E2F2_(+)"    "E2F7_(+)"    "E2F8_(+)"    "EBF1_(+)"   
##  [26] "EGR1_(+)"    "EHF_(+)"     "ELF1_(+)"    "ELF4_(+)"    "ELK3_(+)"   
##  [31] "ELK4_(+)"    "EMX1_(+)"    "ENO1_(+)"    "ERF_(+)"     "ETS1_(+)"   
##  [36] "ETS2_(+)"    "ETV6_(+)"    "ETV7_(+)"    "FOSB_(+)"    "FOSL2_(+)"  
##  [41] "FOXB1_(+)"   "FOXD3_(+)"   "FOXK1_(+)"   "FOXK2_(+)"   "FOXM1_(+)"  
##  [46] "FOXN1_(+)"   "FOXO1_(+)"   "FOXP1_(+)"   "GATA5_(+)"   "GLI1_(+)"   
##  [51] "GRHPR_(+)"   "GSC2_(+)"    "GTF2B_(+)"   "HES6_(+)"    "HEY1_(+)"   
##  [56] "HIVEP2_(+)"  "HLX_(+)"     "HNF4G_(+)"   "HOXA2_(+)"   "HOXA6_(+)"  
##  [61] "HOXA9_(+)"   "HOXB1_(+)"   "HOXB6_(+)"   "HOXC11_(+)"  "HOXC5_(+)"  
##  [66] "HOXC9_(+)"   "HOXD4_(+)"   "HSF1_(+)"    "IKZF2_(+)"   "IRF1_(+)"   
##  [71] "IRF2_(+)"    "IRF5_(+)"    "IRF6_(+)"    "IRF7_(+)"    "IRF8_(+)"   
##  [76] "IRF9_(+)"    "IRX5_(+)"    "JUND_(+)"    "KDM4D_(+)"   "KLF13_(+)"  
##  [81] "KLF5_(+)"    "KLF6_(+)"    "KLF7_(+)"    "LHX1_(+)"    "LHX2_(+)"   
##  [86] "LMX1B_(+)"   "MAFB_(+)"    "MAX_(+)"     "MAZ_(+)"     "MLXIP_(+)"  
##  [91] "MLXIPL_(+)"  "MNX1_(+)"    "MXD3_(+)"    "MYCN_(+)"    "MYEF2_(+)"  
##  [96] "MZF1_(+)"    "NEUROD2_(+)" "NFATC2_(+)"  "NFE2L1_(+)"  "NFE2L2_(+)" 
## [101] "NFKB1_(+)"   "NKX2-2_(+)"  "NKX3-1_(+)"  "NPDC1_(+)"   "NR1D1_(+)"  
## [106] "NR1H3_(+)"   "NR1H4_(+)"   "NR2F1_(+)"   "NR2F6_(+)"   "NR3C2_(+)"  
## [111] "NR4A1_(+)"   "ONECUT2_(+)" "PBX3_(+)"    "PDX1_(+)"    "PHF21A_(+)" 
## [116] "POLE4_(+)"   "POLR3A_(+)"  "POLR3G_(+)"  "POU2F3_(+)"  "POU3F1_(+)" 
## [121] "POU3F4_(+)"  "PPARD_(+)"   "PRDM16_(+)"  "PRRX1_(+)"   "PRRX2_(+)"  
## [126] "REL_(+)"     "RFX1_(+)"    "RFXAP_(+)"   "RUNX2_(+)"   "RXRG_(+)"   
## [131] "SATB1_(+)"   "SETDB1_(+)"  "SHOX2_(+)"   "SIX2_(+)"    "SIX5_(+)"   
## [136] "SMARCA5_(+)" "SMARCC2_(+)" "SNAI3_(+)"   "SOX2_(+)"    "SOX21_(+)"  
## [141] "SOX9_(+)"    "SP6_(+)"     "SREBF1_(+)"  "STAT1_(+)"   "STAT2_(+)"  
## [146] "STAT5B_(+)"  "TAF1_(+)"    "TBX20_(+)"   "TBX3_(+)"    "TCF12_(+)"  
## [151] "TEAD2_(+)"   "TET1_(+)"    "TFAP2A_(+)"  "TFAP2C_(+)"  "TGIF1_(+)"  
## [156] "TP73_(+)"    "TRIM28_(+)"  "TWIST1_(+)"  "USF1_(+)"    "VAX1_(+)"   
## [161] "VEZF1_(+)"   "XBP1_(+)"    "ZBED1_(+)"   "ZBTB41_(+)"  "ZFHX3_(+)"  
## [166] "ZFX_(+)"     "ZNF239_(+)"  "ZNF274_(+)"  "ZNF276_(+)"  "ZNF460_(+)" 
## [171] "ZNF502_(+)"  "ZNF524_(+)"  "ZNF579_(+)"  "ZNF583_(+)"  "ZNF652_(+)" 
## [176] "ZNF668_(+)"  "ZNF672_(+)"  "ZNF701_(+)"  "ZNF721_(+)"  "ZNF730_(+)" 
## [181] "ZNF768_(+)"  "ZNF773_(+)"  "ZNF787_(+)"  "ZXDC_(+)"   
## 
## $SARSCoV2_infected_Calu3
##   [1] "AKR1A1_(+)"       "ALX4_(+)"         "AR_(+)"          
##   [4] "ARID3C_(+)"       "ARID5B_(+)"       "ARNT_(+)"        
##   [7] "ARNT2_(+)"        "ARNTL_(+)"        "ARNTL2_(+)"      
##  [10] "ARX_(+)"          "ASCL1_(+)"        "ASCL2_(+)"       
##  [13] "ATF3_(+)"         "ATF4_(+)"         "ATF6_(+)"        
##  [16] "ATF6B_(+)"        "BACH2_(+)"        "BATF_(+)"        
##  [19] "BBX_(+)"          "BCL11A_(+)"       "BCL3_(+)"        
##  [22] "BDP1_(+)"         "BHLHE40_(+)"      "BHLHE41_(+)"     
##  [25] "BNC2_(+)"         "BORCS8-MEF2B_(+)" "BRCA1_(+)"       
##  [28] "BRF2_(+)"         "CCNT2_(+)"        "CDX2_(+)"        
##  [31] "CEBPD_(+)"        "CEBPG_(+)"        "CIC_(+)"         
##  [34] "CPEB1_(+)"        "CREB3L1_(+)"      "CREB5_(+)"       
##  [37] "CREBL2_(+)"       "CTCF_(+)"         "CUX1_(+)"        
##  [40] "DBP_(+)"          "DDIT3_(+)"        "DLX2_(+)"        
##  [43] "DLX3_(+)"         "DLX4_(+)"         "DMRT1_(+)"       
##  [46] "DRGX_(+)"         "DUX4_(+)"         "DUXA_(+)"        
##  [49] "E2F1_(+)"         "E2F2_(+)"         "E2F8_(+)"        
##  [52] "E4F1_(+)"         "EGR2_(+)"         "EGR3_(+)"        
##  [55] "EHF_(+)"          "ELF1_(+)"         "ELF4_(+)"        
##  [58] "ELK1_(+)"         "ELK3_(+)"         "ELK4_(+)"        
##  [61] "EMX1_(+)"         "ENO1_(+)"         "EOMES_(+)"       
##  [64] "EP300_(+)"        "ESRRA_(+)"        "ESX1_(+)"        
##  [67] "ETS1_(+)"         "ETS2_(+)"         "ETV3_(+)"        
##  [70] "ETV4_(+)"         "ETV6_(+)"         "ETV7_(+)"        
##  [73] "EVX2_(+)"         "FBXL19_(+)"       "FEV_(+)"         
##  [76] "FOSB_(+)"         "FOSL1_(+)"        "FOSL2_(+)"       
##  [79] "FOXA2_(+)"        "FOXA3_(+)"        "FOXC1_(+)"       
##  [82] "FOXC2_(+)"        "FOXD2_(+)"        "FOXD3_(+)"       
##  [85] "FOXD4L6_(+)"      "FOXF1_(+)"        "FOXF2_(+)"       
##  [88] "FOXG1_(+)"        "FOXJ2_(+)"        "FOXJ3_(+)"       
##  [91] "FOXK1_(+)"        "FOXL1_(+)"        "FOXM1_(+)"       
##  [94] "FOXN1_(+)"        "FOXO1_(+)"        "FOXO3_(+)"       
##  [97] "FOXO4_(+)"        "GABPB1_(+)"       "GATA2_(+)"       
## [100] "GATA3_(+)"        "GATA5_(+)"        "GATA6_(+)"       
## [103] "GBX1_(+)"         "GLI1_(+)"         "GLIS2_(+)"       
## [106] "GMEB1_(+)"        "GMEB2_(+)"        "GRHL1_(+)"       
## [109] "GRHL2_(+)"        "GRHPR_(+)"        "GSC_(+)"         
## [112] "GSC2_(+)"         "GTF2B_(+)"        "GTF2IRD1_(+)"    
## [115] "GTF3A_(+)"        "HAND1_(+)"        "HDAC2_(+)"       
## [118] "HES1_(+)"         "HES5_(+)"         "HES6_(+)"        
## [121] "HESX1_(+)"        "HEY2_(+)"         "HINFP_(+)"       
## [124] "HIVEP1_(+)"       "HIVEP2_(+)"       "HLF_(+)"         
## [127] "HLX_(+)"          "HMGB1_(+)"        "HNF1A_(+)"       
## [130] "HOXA2_(+)"        "HOXA6_(+)"        "HOXA9_(+)"       
## [133] "HOXB4_(+)"        "HOXB6_(+)"        "HOXB7_(+)"       
## [136] "HOXB8_(+)"        "HOXB9_(+)"        "HOXC10_(+)"      
## [139] "HOXC11_(+)"       "HOXC13_(+)"       "HOXC4_(+)"       
## [142] "HOXC6_(+)"        "HOXC8_(+)"        "HOXD1_(+)"       
## [145] "HOXD10_(+)"       "HOXD4_(+)"        "HOXD8_(+)"       
## [148] "HOXD9_(+)"        "HSF1_(+)"         "HSF2_(+)"        
## [151] "IKZF2_(+)"        "ING3_(+)"         "IRF1_(+)"        
## [154] "IRF2_(+)"         "IRF4_(+)"         "IRF5_(+)"        
## [157] "IRF6_(+)"         "IRF7_(+)"         "IRF8_(+)"        
## [160] "IRF9_(+)"         "IRX2_(+)"         "ISL2_(+)"        
## [163] "JUN_(+)"          "JUND_(+)"         "KDM4D_(+)"       
## [166] "KDM5A_(+)"        "KLF10_(+)"        "KLF11_(+)"       
## [169] "KLF12_(+)"        "KLF13_(+)"        "KLF14_(+)"       
## [172] "KLF15_(+)"        "KLF16_(+)"        "KLF2_(+)"        
## [175] "KLF5_(+)"         "KLF6_(+)"         "KLF7_(+)"        
## [178] "KLF8_(+)"         "KLF9_(+)"         "LBX1_(+)"        
## [181] "LHX1_(+)"         "LHX4_(+)"         "LHX5_(+)"        
## [184] "LMX1B_(+)"        "MAFA_(+)"         "MAFB_(+)"        
## [187] "MAFK_(+)"         "MAX_(+)"          "MAZ_(+)"         
## [190] "MECOM_(+)"        "MEF2C_(+)"        "MEIS1_(+)"       
## [193] "MEOX2_(+)"        "MESP1_(+)"        "MIOS_(+)"        
## [196] "MITF_(+)"         "MLXIP_(+)"        "MLXIPL_(+)"      
## [199] "MXI1_(+)"         "MYBL1_(+)"        "MYCN_(+)"        
## [202] "MYEF2_(+)"        "MYOD1_(+)"        "MYPOP_(+)"       
## [205] "MZF1_(+)"         "NEUROD1_(+)"      "NFATC2_(+)"      
## [208] "NFE2_(+)"         "NFE2L1_(+)"       "NFE2L2_(+)"      
## [211] "NFE2L3_(+)"       "NFIC_(+)"         "NFKB1_(+)"       
## [214] "NFYA_(+)"         "NFYC_(+)"         "NHLH1_(+)"       
## [217] "NHLH2_(+)"        "NKX3-1_(+)"       "NKX6-2_(+)"      
## [220] "NPAS2_(+)"        "NPDC1_(+)"        "NR0B1_(+)"       
## [223] "NR1H2_(+)"        "NR1H3_(+)"        "NR1H4_(+)"       
## [226] "NR1I2_(+)"        "NR2E1_(+)"        "NR2F1_(+)"       
## [229] "NR2F6_(+)"        "NR4A1_(+)"        "NR5A2_(+)"       
## [232] "NRF1_(+)"         "OLIG2_(+)"        "OLIG3_(+)"       
## [235] "ONECUT2_(+)"      "OTP_(+)"          "OVOL1_(+)"       
## [238] "PAX7_(+)"         "PAX8_(+)"         "PAX9_(+)"        
## [241] "PBX1_(+)"         "PDX1_(+)"         "PHF2_(+)"        
## [244] "PHF21A_(+)"       "PHF8_(+)"         "PHOX2A_(+)"      
## [247] "PKNOX1_(+)"       "POLE3_(+)"        "POLR2A_(+)"      
## [250] "POLR3A_(+)"       "POU2F1_(+)"       "POU4F1_(+)"      
## [253] "POU5F1_(+)"       "POU5F1B_(+)"      "POU6F1_(+)"      
## [256] "PPARA_(+)"        "PPARD_(+)"        "PRDM1_(+)"       
## [259] "PRDM16_(+)"       "PRRX1_(+)"        "PRRX2_(+)"       
## [262] "RAD21_(+)"        "RARA_(+)"         "RARG_(+)"        
## [265] "RBBP5_(+)"        "REL_(+)"          "RFX7_(+)"        
## [268] "RREB1_(+)"        "RUNX2_(+)"        "SATB1_(+)"       
## [271] "SETDB1_(+)"       "SHOX2_(+)"        "SIN3A_(+)"       
## [274] "SIX1_(+)"         "SIX2_(+)"         "SIX5_(+)"        
## [277] "SMAD1_(+)"        "SMARCA5_(+)"      "SMARCC2_(+)"     
## [280] "SMC3_(+)"         "SNAI3_(+)"        "SNAPC4_(+)"      
## [283] "SOX11_(+)"        "SOX13_(+)"        "SOX15_(+)"       
## [286] "SOX2_(+)"         "SOX21_(+)"        "SOX4_(+)"        
## [289] "SOX9_(+)"         "SP1_(+)"          "SP2_(+)"         
## [292] "SP6_(+)"          "SP7_(+)"          "SP9_(+)"         
## [295] "SPDEF_(+)"        "SREBF2_(+)"       "SRF_(+)"         
## [298] "STAT1_(+)"        "STAT2_(+)"        "STAT4_(+)"       
## [301] "STAT5B_(+)"       "STAU2_(+)"        "TAF7_(+)"        
## [304] "TAL1_(+)"         "TBP_(+)"          "TBPL2_(+)"       
## [307] "TBX15_(+)"        "TBX18_(+)"        "TBX20_(+)"       
## [310] "TBX6_(+)"         "TCF3_(+)"         "TCF4_(+)"        
## [313] "TCF7_(+)"         "TCF7L1_(+)"       "TEAD4_(+)"       
## [316] "TET1_(+)"         "TFAP2A_(+)"       "TFAP2C_(+)"      
## [319] "TFDP1_(+)"        "TFDP2_(+)"        "TFE3_(+)"        
## [322] "TFEB_(+)"         "TGIF2_(+)"        "THAP1_(+)"       
## [325] "TLX1_(+)"         "TLX2_(+)"         "TP73_(+)"        
## [328] "TRIM28_(+)"       "UBP1_(+)"         "USF1_(+)"        
## [331] "VAX1_(+)"         "VAX2_(+)"         "VDR_(+)"         
## [334] "VEZF1_(+)"        "VSX1_(+)"         "VSX2_(+)"        
## [337] "WT1_(+)"          "YBX1_(+)"         "YY2_(+)"         
## [340] "ZBTB33_(+)"       "ZEB1_(+)"         "ZFHX2_(+)"       
## [343] "ZFY_(+)"          "ZNF134_(+)"       "ZNF143_(+)"      
## [346] "ZNF160_(+)"       "ZNF208_(+)"       "ZNF219_(+)"      
## [349] "ZNF25_(+)"        "ZNF264_(+)"       "ZNF267_(+)"      
## [352] "ZNF276_(+)"       "ZNF316_(+)"       "ZNF354C_(+)"     
## [355] "ZNF384_(+)"       "ZNF429_(+)"       "ZNF441_(+)"      
## [358] "ZNF471_(+)"       "ZNF483_(+)"       "ZNF486_(+)"      
## [361] "ZNF513_(+)"       "ZNF524_(+)"       "ZNF550_(+)"      
## [364] "ZNF554_(+)"       "ZNF560_(+)"       "ZNF606_(+)"      
## [367] "ZNF607_(+)"       "ZNF668_(+)"       "ZNF672_(+)"      
## [370] "ZNF713_(+)"       "ZNF717_(+)"       "ZNF721_(+)"      
## [373] "ZNF761_(+)"       "ZNF768_(+)"       "ZNF787_(+)"      
## [376] "ZNF8_(+)"         "ZSCAN31_(+)"      "ZXDC_(+)"        
## 
## $SARSCoV2_infected_NHBE
##   [1] "AHCTF1_(+)"  "AIRE_(+)"    "ALX1_(+)"    "ARID5B_(+)"  "ARNT_(+)"   
##   [6] "ATF1_(+)"    "BATF_(+)"    "BBX_(+)"     "BCL3_(+)"    "BCL6B_(+)"  
##  [11] "CEBPB_(+)"   "CEBPG_(+)"   "CKMT1B_(+)"  "CREB1_(+)"   "CREB3_(+)"  
##  [16] "CREBL2_(+)"  "DLX4_(+)"    "DMRT1_(+)"   "DMRTA1_(+)"  "DUXA_(+)"   
##  [21] "EBF1_(+)"    "EGR2_(+)"    "ERF_(+)"     "ESRRA_(+)"   "ETV1_(+)"   
##  [26] "ETV6_(+)"    "ETV7_(+)"    "FOSL1_(+)"   "FOXA2_(+)"   "FOXF2_(+)"  
##  [31] "FOXK2_(+)"   "FOXP3_(+)"   "FOXQ1_(+)"   "GATA2_(+)"   "GATA3_(+)"  
##  [36] "HDAC2_(+)"   "HES5_(+)"    "HLF_(+)"     "HNF1A_(+)"   "HNF1B_(+)"  
##  [41] "HOXA2_(+)"   "HOXA5_(+)"   "HOXA7_(+)"   "HOXA9_(+)"   "HOXB5_(+)"  
##  [46] "HOXB6_(+)"   "HOXB7_(+)"   "HOXB8_(+)"   "HOXB9_(+)"   "HOXC10_(+)" 
##  [51] "HOXC4_(+)"   "HOXC5_(+)"   "HOXC6_(+)"   "HOXC8_(+)"   "HSF2_(+)"   
##  [56] "ING3_(+)"    "IRF1_(+)"    "IRF3_(+)"    "IRF4_(+)"    "IRF5_(+)"   
##  [61] "IRF8_(+)"    "IRF9_(+)"    "IRX2_(+)"    "ISL2_(+)"    "JUN_(+)"    
##  [66] "KLF10_(+)"   "KLF5_(+)"    "LHX1_(+)"    "LHX4_(+)"    "LHX8_(+)"   
##  [71] "LHX9_(+)"    "MAFF_(+)"    "MEOX2_(+)"   "MIOS_(+)"    "MLXIP_(+)"  
##  [76] "MSX1_(+)"    "MSX2_(+)"    "MXD4_(+)"    "MYEF2_(+)"   "NFIL3_(+)"  
##  [81] "NFYB_(+)"    "NHLH1_(+)"   "NKX2-1_(+)"  "NKX3-1_(+)"  "NR1I2_(+)"  
##  [86] "NR4A1_(+)"   "NRF1_(+)"    "ONECUT2_(+)" "OVOL2_(+)"   "PAX2_(+)"   
##  [91] "PAX7_(+)"    "PBX1_(+)"    "PDX1_(+)"    "PKNOX1_(+)"  "POU2F3_(+)" 
##  [96] "PRDM16_(+)"  "RARG_(+)"    "RBBP5_(+)"   "RELA_(+)"    "RFX5_(+)"   
## [101] "SIX2_(+)"    "SMC3_(+)"    "SOX13_(+)"   "SOX2_(+)"    "SP1_(+)"    
## [106] "SP2_(+)"     "SP4_(+)"     "SP7_(+)"     "SREBF2_(+)"  "STAT1_(+)"  
## [111] "STAT2_(+)"   "TAF7_(+)"    "TAGLN2_(+)"  "TAL1_(+)"    "TBP_(+)"    
## [116] "TBPL1_(+)"   "TBPL2_(+)"   "TBX15_(+)"   "TBX3_(+)"    "TCF7_(+)"   
## [121] "TET1_(+)"    "TFAP2A_(+)"  "TFE3_(+)"    "TFEB_(+)"    "TLX3_(+)"   
## [126] "TWIST1_(+)"  "UBTF_(+)"    "UQCRB_(+)"   "VSX1_(+)"    "WT1_(+)"    
## [131] "ZEB1_(+)"    "ZFHX2_(+)"   "ZFY_(+)"     "ZNF160_(+)"  "ZNF471_(+)" 
## [136] "ZNF502_(+)"  "ZNF560_(+)"  "ZNF580_(+)"  "ZNF768_(+)"  "ZNF773_(+)" 
## [141] "ZXDC_(+)"   
## 
## $human_IFNB_treated_NHBE
##  [1] "ATF3_(+)"    "BACH2_(+)"   "ELF3_(+)"    "ETV6_(+)"    "ETV7_(+)"   
##  [6] "FOXA1_(+)"   "FOXK1_(+)"   "GATA2_(+)"   "GCM1_(+)"    "GTF2B_(+)"  
## [11] "HIVEP2_(+)"  "HLX_(+)"     "HOXD11_(+)"  "IRF1_(+)"    "IRF2_(+)"   
## [16] "IRF7_(+)"    "IRF8_(+)"    "IRF9_(+)"    "NFIL3_(+)"   "NFIX_(+)"   
## [21] "NKX3-1_(+)"  "POU5F1B_(+)" "PRDM16_(+)"  "RARA_(+)"    "RELA_(+)"   
## [26] "RXRB_(+)"    "SOX11_(+)"   "SOX9_(+)"    "STAT2_(+)"   "TFEB_(+)"   
## [31] "VEZF1_(+)"

References

[1] https://www.cienciadedatos.net/documentos/19b_comparaciones_multiples_correccion_p-value_fdr

[2] https://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-go.html

sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=es_MX.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=es_MX.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=es_MX.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] parallel  stats4    grid      stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] clusterProfiler_4.0.5 ggrepel_0.9.1         enrichplot_1.12.3    
##  [4] ggpubr_0.4.0.999      org.Hs.eg.db_3.13.0   AnnotationDbi_1.54.1 
##  [7] IRanges_2.26.0        S4Vectors_0.30.2      Biobase_2.52.0       
## [10] BiocGenerics_0.38.0   RColorBrewer_1.1-2    circlize_0.4.14      
## [13] ComplexHeatmap_2.8.0  forcats_0.5.1         stringr_1.4.0        
## [16] dplyr_1.0.9           purrr_0.3.4           readr_2.1.2          
## [19] tidyr_1.2.0           tibble_3.1.7          ggplot2_3.3.5        
## [22] tidyverse_1.3.1      
## 
## loaded via a namespace (and not attached):
##   [1] shadowtext_0.1.1       readxl_1.4.0           backports_1.4.1       
##   [4] fastmatch_1.1-3        plyr_1.8.7             igraph_1.2.11         
##   [7] lazyeval_0.2.2         splines_4.1.1          BiocParallel_1.26.2   
##  [10] GenomeInfoDb_1.28.4    digest_0.6.29          yulab.utils_0.0.4     
##  [13] foreach_1.5.2          htmltools_0.5.2        GOSemSim_2.18.1       
##  [16] viridis_0.6.2          GO.db_3.13.0           fansi_1.0.3           
##  [19] magrittr_2.0.3         memoise_2.0.1          cluster_2.1.2         
##  [22] doParallel_1.0.17      tzdb_0.3.0             Biostrings_2.60.2     
##  [25] graphlayouts_0.8.0     modelr_0.1.8           matrixStats_0.61.0    
##  [28] vroom_1.5.7            colorspace_2.0-3       blob_1.2.2            
##  [31] rvest_1.0.2            haven_2.4.3            xfun_0.31             
##  [34] crayon_1.5.1           RCurl_1.98-1.6         jsonlite_1.8.0        
##  [37] scatterpie_0.1.7       ape_5.6-2              iterators_1.0.14      
##  [40] glue_1.6.2             polyclip_1.10-0        gtable_0.3.0          
##  [43] zlibbioc_1.38.0        XVector_0.32.0         GetoptLong_1.0.5      
##  [46] car_3.0-12             shape_1.4.6            abind_1.4-5           
##  [49] scales_1.1.1           DOSE_3.18.3            DBI_1.1.2             
##  [52] rstatix_0.7.0          Rcpp_1.0.8.3           viridisLite_0.4.0     
##  [55] clue_0.3-60            tidytree_0.3.9         gridGraphics_0.5-1    
##  [58] bit_4.0.4              httr_1.4.3             fgsea_1.18.0          
##  [61] ellipsis_0.3.2         pkgconfig_2.0.3        farver_2.1.0          
##  [64] sass_0.4.1             dbplyr_2.1.1           utf8_1.2.2            
##  [67] labeling_0.4.2         ggplotify_0.1.0        tidyselect_1.1.2      
##  [70] rlang_1.0.2            reshape2_1.4.4         munsell_0.5.0         
##  [73] cellranger_1.1.0       tools_4.1.1            cachem_1.0.6          
##  [76] downloader_0.4         cli_3.3.0              generics_0.1.2        
##  [79] RSQLite_2.2.11         broom_0.7.12           evaluate_0.15         
##  [82] fastmap_1.1.0          yaml_2.3.5             ggtree_3.0.4          
##  [85] knitr_1.39             bit64_4.0.5            fs_1.5.2              
##  [88] tidygraph_1.2.0        KEGGREST_1.32.0        ggraph_2.0.5          
##  [91] nlme_3.1-152           aplot_0.1.2            DO.db_2.9             
##  [94] xml2_1.3.3             compiler_4.1.1         rstudioapi_0.13       
##  [97] png_0.1-7              ggsignif_0.6.3         treeio_1.16.2         
## [100] reprex_2.0.1           tweenr_1.0.2           bslib_0.3.1           
## [103] stringi_1.7.6          highr_0.9              lattice_0.20-44       
## [106] Matrix_1.3-4           vctrs_0.4.1            pillar_1.7.0          
## [109] lifecycle_1.0.1        jquerylib_0.1.4        GlobalOptions_0.1.2   
## [112] cowplot_1.1.1          data.table_1.14.2      bitops_1.0-7          
## [115] patchwork_1.1.1        qvalue_2.24.0          R6_2.5.1              
## [118] gridExtra_2.3          codetools_0.2-18       MASS_7.3-54           
## [121] assertthat_0.2.1       rjson_0.2.21           withr_2.5.0           
## [124] GenomeInfoDbData_1.2.6 hms_1.1.1              ggfun_0.0.5           
## [127] rmarkdown_2.14         carData_3.0-5          Cairo_1.5-15          
## [130] ggforce_0.3.3          lubridate_1.8.0